Benign lipomatous neoplasm of intrathoracic organs

CD2_BENIGN_LIPO_INTRA_ABD

kidney neoplasm: A benign or malignant neoplasm affecting the kidney. Representative examples of benign renal neoplasms include fibroma, lipoma, oncocytoma, and juxtaglomerular cell tumor. Representative examples of malignant renal neoplasms include renal cell carcinoma, renal pelvis carcinoma, Wilms tumor, rhabdoid tumor, sarcoma, and lymphoma.

Suggest a new description

Endpoint definition

↥

Endpoint definition steps	FinnGen
Phenotype data	520210
1. Apply sex-specific rule None	520210
2. Check conditions None	520210
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Hospital discharge: ICD-10 — D17.4& Cause of death: ICD-10 — D17.4& 2 out of 7 registries used, show all original rules.	51
4. Check minimum number of events None	51
5. Include endpoints None	51
6. Filter based on genotype QC (FinnGen only)	51

Control definitions (FinnGen only)

Controls for this endpoint are individuals that are not cases.

Extra metadata

Level in the ICD hierarchy: 3
First used in FinnGen datafreeze: DF2
Parent code in ICD-10: D17
Name in latin: Neoplasma benignum lipomatosum organorum intrathoracalium

NAME	CD2_BENIGN_LIPO_INTRA_ABD
CONTROL_EXCLUDE
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	D174
HD_ICD_9	$!$	The FinnGen clinical team has checked and no code can be used for this rule.
HD_ICD_8	$!$	The FinnGen clinical team has checked and no code can be used for this rule.
HD_ICD_10_EXCL
HD_ICD_9_EXCL
HD_ICD_8_EXCL
COD_MAINONLY
COD_ICD_10	D174
COD_ICD_9	$!$	The FinnGen clinical team has checked and no code can be used for this rule.
COD_ICD_8	$!$	The FinnGen clinical team has checked and no code can be used for this rule.
COD_ICD_10_EXCL
COD_ICD_9_EXCL
COD_ICD_8_EXCL
OPER_NOM
OPER_HL
OPER_HP1
OPER_HP2
KELA_REIMB
KELA_REIMB_ICD
KELA_ATC_NEEDOTHER
KELA_ATC
KELA_VNRO_NEEDOTHER
KELA_VNRO
CANC_TOPO
CANC_TOPO_EXCL
CANC_MORPH
CANC_MORPH_EXCL
CANC_BEHAV

Similar endpoints

↥

List of similar endpoints to Benign lipomatous neoplasm of intrathoracic organs based on the number of shared cases.

Similar with more cases:

Similar with less cases:

Benign lipomatous neoplasm of intrathoracic organs

Case counts by codes

↥

FinnGen case counts by registry codes:

Upset plot

Full data table

Summary Statistics

↥

-FinRegistry-

Key figures

	All	Female	Male
Number of individuals
Whole population	300	167	131
Only index persons	271	155	116
Unadjusted period prevalence (%)
Whole population	0.00	0.00	0.00
Only index persons	0.01	0.01	0.00
Median age at first event (years)
Whole population	57.92	58.06	57.67
Only index persons	57.34	57.73	56.82

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	51	33	18
Unadjusted period prevalence (%)	0.01	0.01	0.01
Median age at first event (years)	53.54	53.23	54.11

-FinRegistry-

Age distribution of first events

-FinnGen-

Age distribution of first events

-FinRegistry-

Year distribution of first events

-FinnGen-

Year distribution of first events

-FinRegistry-

Cumulative Incidence Function

No data

-FinnGen-

Cumulative Incidence Function

Not a core endpoint, no data to show.

CodeWAS (R11)

↥

CodeWAS is a tool for exploring the associations between an endpoint and all of the medical codes and drug codes.

This is a new tool, please reach out using the contact form for feedback and improvement ideas.

First, a cohort is built by matching controls to the endpoint cases using year of birth and sex. Then, a Fisher test is done for all the medical codes and drug codes between the cases and controls of this cohort. Codes are reported in the table below if they have −log₁₀(p-value) ≥ 6.

No data available

LabWAS

↥

(ID) Name

N Cases

N Controls

-log₁₀(p)

cases

controls

cases

controls

unit

-log₁₀(p)

N cases

N controls

(3003327) Ova and parasites identified in Stool by Light microscopy

4.38

2.10

1.2

1.1

—

(46235759) Influenza virus B RNA [Presence] in Nasopharynx by NAA with probe detection

4.49

1.87

1.2

2.0

—

(3044938) Influenza virus A RNA [Presence] in Specimen by NAA with probe detection

2.40

1.65

1.8

—

(36304419) Bacteria [Presence] in Urine

106

2.08

1.56

2.0

2.7

—

(586526) SARS-CoV-2 (COVID-19) RNA [Presence] in Nasopharynx by NAA with probe detection

3.57

1.56

1.6

1.3

—

(3002109) Cholesterol in LDL/Cholesterol in HDL [Mass Ratio] in Serum or Plasma

0.00

1.41

0.0

1.5

—

(3048689) Calprotectin [Mass/mass] in Stool

2.27

1.40

1.9

1.7

105.7

92.5

ug/g

0.17

(36031861) Influenza virus A and B and SARS-CoV-2 (COVID-19) and Respiratory syncytial virus RNA panel - Respiratory system specimen by NAA with probe detection

2.96

1.31

2.4

1.7

—

(4010399)

2.58

1.28

1.0

1.4

—

(40768797) Stomach Pathology biopsy report

2.24

1.26

1.1

1.3

—

(3030306) Epithelial cells.non-squamous [#/volume] in Urine by Automated count

2.11

1.26

2.2

2.3

1.5

0.9

e6/l

—

(3026008) Bacteria identified in Urine by Culture

132

1.85

1.22

1.9

2.8

—

(3000067) Parathyrin.intact [Mass/volume] in Serum or Plasma

0.00

1.21

0.0

3.6

—

78.0

—

(3000991) Gas panel - Venous blood

2.37

1.13

4.7

10.3

—

(1761868) Lipid panel - Serum or Plasma

164

0.51

1.04

2.7

2.9

—

(40768804) Tissue Pathology biopsy report

184

1.70

1.02

2.4

1.7

—

(3023520) Reticulocytes [#/volume] in Blood

0.00

1.01

0.0

3.8

—

78.7

—

(3004588) Protein electrophoresis panel - Serum or Plasma

0.00

1.00

0.0

3.7

—

(3043924) Respiratory syncytial virus RNA [Identifier] in Specimen by NAA with probe detection

1.97

0.91

2.0

1.5

—

(3018095) Leukocytes [#/volume] in Urine

143

1.66

0.89

3.3

3.1

30.6

44.0

e6/l

0.19

105

(3008486) Thyroxine (T4) free [Moles/volume] in Serum or Plasma

332

1.74

0.86

3.9

4.3

15.7

15.2

pmol/l

0.48

302

(3007853) Bacteria identified in Skin by Aerobe culture

1.83

0.85

1.3

—

(43054914) Glucose tolerance 2 hours panel - Serum or Plasma

1.92

0.82

1.3

1.8

—

(3044491) Cholesterol non HDL [Mass/volume] in Serum or Plasma

0.00

0.80

0.0

1.3

—

(3030467) Casts [#/volume] in Urine by Automated count

111

1.64

0.78

2.1

2.8

0.9

0.3

e6/l

0.34

(46236098) ABO and Rh group [Type] in Blood by Confirmatory method

1.65

0.74

2.6

2.1

—

(3002582) Erythrocytes [#/volume] in Urine

122

1.59

0.72

1.9

2.8

24.8

23.2

e6/l

—

(3029287) Urinalysis microscopic panel [#/volume] - Urine by Automated count

141

1.55

0.70

1.8

2.7

—

(3038288) Influenza virus B RNA [Presence] in Specimen by NAA with probe detection

1.73

0.70

1.9

1.6

—

(3001079) Blood group antibody screen [Presence] in Serum or Plasma

199

1.50

0.67

2.6

4.0

—

(3018418) pH of Serum or Plasma

127

1.51

0.60

2.1

4.6

7.4

—

(3013650) Neutrophils [#/volume] in Blood by Automated count

253

1.45

0.57

7.2

10.8

4.3

4.0

e9/l

0.30

228

(3044640) Blood type and Crossmatch panel - Blood

129

1.48

0.55

2.4

2.1

—

(21494755) Public health laboratory ask at order entry panel

1.57

0.53

1.2

1.3

—

(3000494) Fungus identified in Specimen by Culture

1.60

0.51

1.6

—

(3015377) Calcium [Moles/volume] in Serum or Plasma

151

1.41

0.48

3.4

2.9

2.4

mmol/l

0.66

127

(3003694) ABO and Rh group [Type] in Blood

112

0.66

0.43

1.0

1.4

—

(3041942) Cyclic citrullinated peptide Ab [Units/volume] in Serum

1.51

0.43

1.6

1.2

41.6

11.3

u/ml

—

(3000492) Spirometry study

1.57

0.42

1.4

1.5

—

(36032419) SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Immunoassay

0.00

0.42

0.0

2.3

—

(3002179) Metamyelocytes/100 leukocytes in Blood

1.52

0.41

2.0

3.6

—

0.8

—

(3000330) Specific gravity of Urine by Test strip

0.00

0.40

0.0

3.6

—

(3043723) Beta 1 globulin [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.40

0.0

3.7

—

(3025159) Blasts/100 leukocytes in Blood

1.47

0.40

3.6

—

0.0

—

(3002256) Pathology report gross observation

1.38

0.35

1.3

1.2

—

(3042936) Bacteria identified in Isolate by Culture

1.34

0.32

1.4

2.1

—

(3023368) Bacteria identified in Blood by Culture

1.36

0.31

2.8

3.9

—

(3011397) Hemoglobin [Presence] in Urine by Test strip

1.36

0.31

5.7

3.2

—

(3018006) Microscopic observation [Identifier] in Cervix by Cyto stain.thin prep

1.39

0.31

2.2

1.4

—

(46235355) HIV 1 and 2 tests - Meaningful Use set

0.68

0.28

1.4

2.0

—

(3044889) 12 lead EKG panel

302

1.26

0.27

3.6

4.0

—

(3021440) Promyelocytes/100 leukocytes in Blood

1.39

0.24

3.6

3.5

—

0.5

—

(40764999) Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum, Plasma or Blood by Creatinine-based formula (CKD-EPI)

409

1.33

0.24

15.0

12.9

83.9

79.3

ml/min/173m2

1.01

321

(3003338) MCHC [Mass/volume]

366

1.28

0.24

17.6

17.8

331.1

332.0

g/l

0.27

366

(3015736) pH of Urine

175

1.24

0.23

3.9

3.3

—

(706163) SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory system specimen by NAA with probe detection

255

1.22

0.22

3.1

2.8

—

(4035726)

1.21

0.22

1.2

—

(3017181) Myelocytes/100 leukocytes in Blood

1.21

0.22

3.6

3.3

—

1.2

—

(3002434) Lupus erythematosus deoxynucleoproteins IgG Ab [Units/volume] in Serum by Immunoassay

0.00

0.21

0.0

1.5

—

(3002482) Mycoplasma pneumoniae DNA [Presence] in Specimen by NAA with probe detection

0.00

0.21

0.0

1.5

—

(3008037) Lactate [Moles/volume] in Venous blood

0.00

0.21

0.0

2.5

—

1.2

—

(3024403) Complement+Immunoglobulin [Units/volume] in Red Blood Cells

0.00

0.21

0.0

2.3

—

(3021584) Pregnancy associated plasma protein A [Units/volume] in Serum or Plasma

0.00

0.21

0.0

1.5

—

(3040853) Adenovirus DNA [Identifier] in Specimen by NAA with probe detection

0.00

0.21

0.0

2.0

—

(3031478) Chlamydophila pneumoniae DNA [Presence] in Specimen by NAA with probe detection

0.00

0.21

0.0

1.6

—

(3042194) Human metapneumovirus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.21

0.0

2.0

—

(3027944) Amphetamines [Presence] in Urine

0.00

0.21

0.0

1.0

—

(3038515) Glucose [Moles/volume] in Venous blood

0.00

0.21

0.0

2.7

—

7.5

—

(3022145) Colonoscopy Study observation

1.31

0.21

1.3

—

(40760888) Immunoglobulin light chains.free panel - Serum

0.00

0.21

0.0

7.0

—

(3010156) C reactive protein [Mass/volume] in Serum or Plasma by High sensitivity method

0.00

0.21

0.0

1.6

—

1.0

—

(3031040) Bacteria [#/volume] in Urine by Automated count

286

1.21

0.21

4.4

3.9

—

30.2

—

(3017766) Complement C4 [Mass/volume] in Serum or Plasma

0.00

0.21

0.0

1.1

—

0.3

—

(3000620) Complement C3 [Mass/volume] in Serum or Plasma

0.00

0.21

0.0

1.2

—

1.1

—

(1761482) Bacteria [#/volume] in Urine by Culture

0.00

0.21

0.0

4.3

—

(3015171) Extractable nuclear Ab [Units/volume] in Serum

0.00

0.21

0.0

1.4

—

(3049804) Myeloperoxidase IgG Ab [Units/volume] in Serum

0.00

0.20

0.0

1.4

—

(3012336) Haptoglobin [Mass/volume] in Serum or Plasma

0.00

0.20

0.0

3.2

—

1.7

—

(3016771) Amylase [Enzymatic activity/volume] in Serum or Plasma

141

0.81

0.19

4.6

2.3

45.3

52.7

u/l

0.68

127

(3012516) Albumin [Mass/volume] in Urine

120

1.23

0.19

3.0

3.5

7.4

576.2

mg/l

—

(3009542) Hematocrit [Volume Fraction] of Blood

387

1.16

0.09

15.6

14.0

41.1

40.1

0.64

269

(3009035) Cobalamin (Vitamin B12) [Moles/volume] in Serum or Plasma

1.17

0.09

1.6

1.9

790000530.0

497.5

pmol/l

—

(3045783) Sodium and Potassium panel [Moles/volume] - Serum or Plasma

1.09

0.08

6.0

7.4

—

(3032080) INR in Blood by Coagulation assay

167

1.12

0.08

12.1

7.9

1.5

1.2

inr

—

(3024135) Streptococcus.beta-hemolytic [Presence] in Throat by Organism specific culture

0.81

0.08

1.8

1.6

—

(3041096) Erythrocytes [Presence] in Urine by Automated

131

0.89

0.06

2.6

3.2

—

(3020682) Albumin/Creatinine [Ratio] in Urine

129

1.12

0.06

3.9

4.5

4.6

8.0

mg/mmol

—

(40760892) CBC W Ordered Manual Differential panel - Blood

110

1.12

0.05

2.6

5.1

—

(43054903) Holo-transcobalamin II [Moles/volume] in Serum

169

0.92

0.04

1.6

1.8

134.7

96.7

pmol/l

—

(40763086) Leukocyte esterase [Presence] in Urine by Automated test strip

179

0.92

0.04

4.1

3.5

—

(3013512) EKG study

127

0.93

0.02

3.5

3.6

—

(3037467) Urinalysis macro (dipstick) panel - Urine

294

1.05

0.00

4.5

3.7

—

(42870588) Differential panel, method unspecified - Blood

133

0.97

0.00

3.3

5.0

—

(40758558) Short blood count panel - Blood

105

1.06

0.00

3.9

7.5

—

(40761511) CBC panel - Blood by Automated count

459

1.02

0.00

11.1

11.8

—

(3039443) Prostate specific Ag panel - Serum or Plasma

0.00

0.0

1.3

—

(3041354) Potassium [Moles/volume] in Venous blood

0.00

0.0

2.9

—

3.9

—

(3028369) Herpes simplex virus 1+2 DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.3

—

(3019977) pH of Arterial blood

0.00

0.0

2.4

—

(3008757) Leukocyte morphology finding [Identifier] in Blood

0.00

0.0

1.6

—

(40764126) Parainfluenza virus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.2

—

(3024891) Influenza virus A+B Ag [Presence] in Specimen

0.00

0.0

1.2

—

(3020565) Legionella pneumophila DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.4

—

(1616796) Gas panel - Central venous blood

0.00

0.0

2.0

—

(4027681)

0.00

0.0

1.0

—

(3015916) Alpha-1-Fetoprotein [Units/volume] in Serum or Plasma

0.00

0.0

1.7

—

3.6

—

(3051611) Lipemic interference index of Serum or Plasma

0.00

0.0

3.8

—

(21494670) JAK2 gene exon 14 targeted mutation analysis in Blood or Tissue by Molecular genetics method

0.00

0.0

1.0

—

(3019539) Treponema pallidum Ab [Titer] in Serum by Hemagglutination

0.00

0.0

1.2

—

(3000764) Benzodiazepines [Presence] in Urine

0.00

0.0

1.0

—

(3021952) Alkaline phosphatase isoenzymes [Enzymatic activity/volume] in Serum or Plasma by Heat stability

0.00

0.0

1.3

—

(3016879) Cocaine [Presence] in Urine

0.00

0.0

1.0

—

(3011288) Drugs identified in Urine by Screen method

0.00

0.0

1.1

—

(3032035) Polymorphonuclear cells/100 leukocytes in Blood

0.00

0.0

2.6

—

58.7

—

(3043849) Epstein Barr virus DNA [Units/volume] (viral load) in Serum or Plasma by NAA with probe detection

0.00

0.0

1.7

—

(40768795) Lymph node Pathology biopsy report

0.00

0.0

1.1

—

(3042596) Human coronavirus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.3

—

(3023420) DNA double strand Ab [Units/volume] in Serum

0.00

0.0

1.4

—

(3037875) Bordetella parapertussis DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.0

—

(3016724) Homocysteine [Moles/volume] in Serum or Plasma

0.00

0.0

1.5

—

11.7

—

(40768441) Liver Pathology biopsy report

0.00

0.0

1.0

—

(3042111) Morphology [Interpretation] in Bone marrow Narrative

0.00

0.0

3.0

—

(3017817) Protein [Mass] in Urine collected for unspecified duration

0.00

0.0

7.0

—

(40768800) Prostate Pathology biopsy report

0.00

0.0

1.3

—

(3045156) Carbon dioxide [Partial pressure] adjusted to patient's actual temperature in Arterial blood

0.00

0.0

2.4

—

(3037756) Immunofixation for Serum or Plasma

0.00

0.0

1.6

—

(3021788) Differential panel - Synovial fluid

0.00

0.0

1.3

—

(3047007) Chlamydophila sp Ab [Presence] in Serum

0.00

0.0

1.2

—

(4306422)

0.00

0.0

1.2

—

(3046524) Influenza virus A Ag [Presence] in Nasopharynx by Immunoassay

0.00

0.0

1.0

—

(1175715) Chlamydophila pneumoniae IgM Ab [Presence] in Serum by Immunoassay

0.00

0.0

1.2

—

(3014051) Protein [Presence] in Urine by Test strip

0.00

0.0

1.9

—

(3024928) Oxygen saturation in Venous blood

0.00

0.0

2.5

—

(1001926) Buprenorphine [Presence] in Urine by Screen method

0.00

0.0

1.0

—

(3033705) Calcium.ionized [Moles/volume] in Venous blood

0.00

0.0

2.9

—

(3012477) Bordetella pertussis DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.6

—

(43055361) Metamyelocytes/Leukocytes [Pure number fraction] in Blood by Manual count

0.00

0.0

2.3

—

(3027315) Oxygen [Partial pressure] in Blood

0.00

0.0

1.4

—

7.5

—

(3020148) Glutamate decarboxylase 65 Ab [Units/volume] in Serum

0.00

0.0

1.2

—

(3013290) Carbon dioxide [Partial pressure] in Blood

0.00

0.0

1.4

—

5.3

—

(3027008) Opiates [Presence] in Urine

0.00

0.0

1.0

—

(3030905) Polymorphonuclear cells [#/volume] in Blood

0.00

0.0

2.3

—

5.1

—

(3043362) Influenza virus B Ag [Presence] in Nasopharynx by Immunoassay

0.00

0.0

1.0

—

(3050129) First trimester maternal screen panel - Serum or Plasma

0.00

0.0

1.5

—

(3030692) Respiratory virus DNA+RNA [Identifier] in Specimen by NAA with probe detection

0.00

0.0

1.3

—

(3003181) Sodium [Moles/volume] in Urine

0.00

0.0

1.2

—

61.7

—

(3035285) Chloride [Moles/volume] in Venous blood

0.00

0.0

2.9

—

107.1

—

(3004383) Neutrophil cytoplasmic Ab.classic [Titer] in Serum by Immunofluorescence

0.00

0.0

1.0

—

(3003265) Liver kidney microsomal Ab [Titer] in Serum by Immunofluorescence

0.00

0.0

2.0

—

(40765161) Human bocavirus DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.0

—

(3049539) Genetic diseases [Identifier] in Blood or Tissue by FISH Nominal

0.00

0.0

1.0

—

(3015816) F5 gene p.Arg506Gln [Presence] in Blood or Tissue by Molecular genetics method

0.00

0.0

1.0

—

(40760847) Basement membrane Ab [Titer] in Serum by Immunofluorescence

0.00

0.0

1.2

—

(3046294) Neutrophil cytoplasmic Ab.classic [Titer] in Serum

0.00

0.0

1.4

—

(3020717) Zinc [Moles/volume] in Serum or Plasma

0.00

0.0

1.0

—

13.3

—

(3022803) Oxygen [Partial pressure] adjusted to patient's actual temperature in Arterial blood

0.00

0.0

2.4

—

(3028300) Cannabinoids [Presence] in Urine

0.00

0.0

1.0

—

(21494890) Protein electrophoresis panel - 24 hour Urine

0.00

0.0

5.3

—

Mortality – FinRegistry

↥

Association

Association between endpoint CD2_BENIGN_LIPO_INTRA_ABD and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have CD2_BENIGN_LIPO_INTRA_ABD.

N-year risk	Females	Males
1	No data	No data
5	No data	No data
10	No data	No data
15	No data	No data
20	No data	No data

Relationships between endpoints

↥

Index endpoint: CD2_BENIGN_LIPO_INTRA_ABD – Benign lipomatous neoplasm of intrathoracic organs

GWS hits: -

Endpoint

Case Overlap

Survival Analysis

Genetic Correlations

Genetic Signals

N (Jaccard index)

HR [CI]

rg [CI]

Hits

Coloc Hits

FinRegistry

FinnGen

FinRegistry

FinnGen

Loading data

Benign lipomatous neoplasm of intrathoracic organs

Endpoint definition

Endpoint definition steps

FinnGen

Phenotype data

1. Apply sex-specific rule

2. Check conditions

3. Check pre-conditions, main-only, mode, registry filters

4. Check minimum number of events

5. Include endpoints

6. Filter based on genotype QC (FinnGen only)

Similar endpoints

Case counts by codes

Summary Statistics

-FinRegistry-

Key figures

-FinnGen-

Key figures

-FinRegistry-

Age distribution of first events

-FinnGen-

Age distribution of first events

-FinRegistry-

Year distribution of first events

-FinnGen-

Year distribution of first events

-FinRegistry-

Cumulative Incidence Function

-FinnGen-

Cumulative Incidence Function

CodeWAS (R11)

LabWAS

Mortality – FinRegistry

Association

Females

Males

Mortality risk

Relationships between endpoints