Benign neoplasm: Renal pelvis

CD2_BENIGN_RENALPELVIS

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 — D30.1& Hospital discharge: ICD-9 — 2231 Hospital discharge: ICD-8 — 2231 Cause of death: ICD-10 — D30.1& Cause of death: ICD-9 — 2231 Cause of death: ICD-8 — 2231 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: D30
Name in latin: Neoplasma benignum pelvis renalis

NAME	CD2_BENIGN_RENALPELVIS
CONTROL_EXCLUDE
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	D301
HD_ICD_9	2231
HD_ICD_8	2231
HD_ICD_10_EXCL
HD_ICD_9_EXCL
HD_ICD_8_EXCL
COD_MAINONLY
COD_ICD_10	D301
COD_ICD_9	2231
COD_ICD_8	2231
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 neoplasm: Renal pelvis based on the number of shared cases.

Similar with more cases:

Similar with less cases:

Benign neoplasm: Renal pelvis

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	433	243	179
Only index persons	327	197	130
Unadjusted period prevalence (%)
Whole population	0.01	0.01	0.01
Only index persons	0.01	0.01	0.00
Median age at first event (years)
Whole population	66.97	65.17	69.25
Only index persons	65.81	64.03	68.50

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	51	31	20
Unadjusted period prevalence (%)	0.01	0.01	0.01
Median age at first event (years)	61.93	56.36	70.57

-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

No data

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

(3015736) pH of Urine

147

3.01

3.62

4.1

3.7

—

(3016251) Hemoglobin.gastrointestinal [Presence] in Stool

4.54

2.69

2.1

2.2

—

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

285

2.87

2.51

7.0

4.8

—

6599.3

—

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

234

2.58

2.50

8.5

10.0

4.4

4.1

e9/l

0.31

208

(3026782) Osmolality of Urine

2.58

2.44

3.4

2.7

508.5

525.0

mosm/kgh2o

0.10

(3037467) Urinalysis macro (dipstick) panel - Urine

282

2.63

2.25

6.7

4.4

—

(3013139) Helicobacter pylori Ag [Presence] in Stool

4.70

2.22

1.2

1.4

—

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

150

2.31

2.19

5.5

3.0

—

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

2.47

2.17

3.6

4.6

—

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

187

2.28

2.13

5.7

4.2

—

(3049717) Cytology report of Urine Cyto stain

3.85

1.90

3.8

2.6

—

(3013115) Eosinophils [#/volume] in Blood

198

2.08

1.73

5.2

5.8

0.2

e9/l

0.04

178

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

128

2.09

1.68

3.5

2.7

62.1

58.6

u/l

0.22

120

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

155

2.04

1.64

2.4

1.9

87.3

98.9

pmol/l

—

(3016417) Amylase.pancreatic [Enzymatic activity/volume] in Serum or Plasma

2.73

1.57

1.8

2.4

24.6

28.0

u/l

—

(3003338) MCHC [Mass/volume]

315

2.25

1.56

30.1

20.7

329.6

331.1

g/l

0.38

315

(3029879) Epithelial cells.squamous [#/volume] in Urine by Automated count

2.31

1.53

5.3

2.6

0.4

2.0

e6/l

—

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

116

2.02

1.49

5.9

2.9

0.0

0.7

e6/l

1.59

(3019198) Lymphocytes [#/volume] in Blood

198

1.92

1.43

5.7

5.9

1.7

1.8

e9/l

0.17

179

(3002256) Pathology report gross observation

2.35

1.38

1.2

1.3

—

(3006315) Basophils [#/volume] in Blood

191

1.88

1.36

5.5

5.9

0.0

e9/l

0.71

169

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

2.14

1.31

5.3

2.5

0.6

e6/l

—

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

1.97

1.29

3.8

2.3

—

(3009542) Hematocrit [Volume Fraction] of Blood

326

2.05

1.26

26.0

15.8

35.8

38.5

0.68

231

(36304419) Bacteria [Presence] in Urine

114

1.89

1.25

5.9

2.9

—

(3044640) Blood type and Crossmatch panel - Blood

132

1.85

1.22

3.7

2.3

—

(3012516) Albumin [Mass/volume] in Urine

107

1.88

1.19

5.1

2.9

36.7

111.5

mg/l

—

(4010399)

2.66

1.18

1.8

1.4

—

(40762366) Oxygen capacity [Volume Fraction] in Arterial blood

2.53

1.11

7.8

7.7

—

(3044889) 12 lead EKG panel

280

1.80

1.08

4.7

4.0

—

(3023368) Bacteria identified in Blood by Culture

119

1.79

1.07

4.1

4.6

—

(3018251) Fasting glucose [Moles/volume] in Serum or Plasma

382

2.10

1.07

5.2

4.6

6.0

5.9

mmol/l

0.10

354

(3001604) Monocytes [#/volume] in Blood

192

1.72

1.06

5.6

5.8

0.6

e9/l

0.07

168

(3026008) Bacteria identified in Urine by Culture

137

1.76

1.06

3.8

3.3

—

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

146

1.75

1.06

5.8

4.4

—

(3037522) Nuclear Ab [Titer] in Serum

2.01

1.05

1.3

1.4

—

432.0

—

(3020682) Albumin/Creatinine [Ratio] in Urine

111

1.80

1.05

6.4

3.5

5.7

14.4

mg/mmol

—

(3021589) Normoblasts [#/volume] in Blood

167

1.69

0.98

6.6

11.0

0.0

e9/l

0.00

136

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

1.75

0.91

1.6

1.3

—

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

1.92

0.89

9.8

—

(3042936) Bacteria identified in Isolate by Culture

1.90

0.87

1.9

2.0

—

(40761535) Cells panel - Urine sediment

1.99

0.85

2.3

4.2

—

(40761511) CBC panel - Blood by Automated count

402

2.01

0.84

17.0

14.7

—

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

211

1.59

0.83

2.8

2.9

—

(3022621) pH of Urine by Test strip

1.92

0.82

6.0

2.9

—

(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

2.20

0.77

1.8

1.3

—

(40768804) Tissue Pathology biopsy report

157

1.57

0.76

2.9

2.0

—

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

1.80

0.75

1.7

1.4

—

(3012544) pH of Venous blood

1.82

0.73

5.0

3.2

—

(3021879) Hepatitis B virus core Ab [Presence] in Serum

1.94

0.70

1.2

1.4

—

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

1.94

0.70

1.2

1.7

—

(3007853) Bacteria identified in Skin by Aerobe culture

1.68

0.68

3.6

1.3

—

(3000963) Hemoglobin [Mass/volume] in Blood

428

1.76

0.51

33.1

23.3

129.4

132.2

g/l

0.88

422

(3035941) MCH [Entitic mass]

428

1.76

0.51

32.9

23.1

30.4

0.10

422

(3024731) MCV [Entitic volume]

428

1.76

0.51

33.0

23.1

92.1

91.5

0.40

422

(3019800) Troponin T.cardiac [Mass/volume] in Serum or Plasma

171

1.39

0.46

4.2

4.7

31.6

81.5

ng/l

0.97

124

(3004789) Transferrin [Mass/volume] in Serum or Plasma

1.48

0.45

3.4

2.6

2.0

2.3

g/l

—

(3019284) Hepatitis B virus surface Ag [Presence] in Serum

1.45

0.44

1.8

1.4

—

(3004588) Protein electrophoresis panel - Serum or Plasma

1.62

0.43

1.6

2.8

—

(40758558) Short blood count panel - Blood

107

1.43

0.43

5.1

6.9

—

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

1.39

0.43

1.9

1.6

—

(4094501)

0.00

0.42

0.0

1.3

—

(3006184) Hemoglobin [Mass/volume] in Capillary blood

0.00

0.42

0.0

2.8

—

118.9

—

(3021614) Rheumatoid factor [Units/volume] in Serum or Plasma

1.44

0.41

1.4

1.3

—

23.9

—

(3000991) Gas panel - Venous blood

1.47

0.40

9.6

7.3

—

(42870588) Differential panel, method unspecified - Blood

128

1.36

0.38

5.6

5.4

—

(3022145) Colonoscopy Study observation

1.48

0.37

1.2

1.3

—

(3017143) Hepatitis C virus Ab [Presence] in Serum

1.38

0.35

1.8

1.5

—

(3019225) pH of Specimen

1.34

0.34

7.0

4.3

—

(40763571) Iron/Transferrin [Ratio] in Serum or Plasma

1.34

0.32

3.4

2.6

20.0

25.1

—

(3013512) EKG study

124

1.30

0.28

3.5

4.0

—

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

1.30

0.28

1.1

1.2

—

(3020564) Creatinine [Moles/volume] in Serum or Plasma

416

1.42

0.25

29.8

18.7

86.1

80.0

umol/l

0.56

416

(3041096) Erythrocytes [Presence] in Urine by Automated

107

1.29

0.25

4.4

3.4

—

(3020630) Protein [Mass/volume] in Serum or Plasma

1.35

0.24

1.6

3.3

68.4

67.9

g/l

—

(36305247) Microscopic observation [Identifier] in Isolate by Gram stain

0.00

0.21

0.0

1.5

—

(3022806) Fractional oxyhemoglobin in Capillary blood

0.00

0.21

0.0

1.5

—

88.8

—

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

0.00

0.21

0.0

1.2

—

(3005702) Mycobacterium sp identified in Specimen by Organism specific culture

0.00

0.21

0.0

1.0

—

(3013290) Carbon dioxide [Partial pressure] in Blood

0.00

0.21

0.0

3.4

—

4.8

—

(3027315) Oxygen [Partial pressure] in Blood

0.00

0.21

0.0

3.4

—

8.0

—

(3011371) Neisseria gonorrhoeae DNA [Presence] in Specimen by NAA with probe detection

0.00

0.21

0.0

1.1

—

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

0.00

0.21

0.0

2.6

—

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

0.00

0.21

0.0

1.7

—

(1616796) Gas panel - Central venous blood

0.00

0.21

0.0

3.2

—

(3050380) Cytology report of Cervical or vaginal smear or scraping Cyto stain

0.00

0.21

0.0

1.2

—

(3020961) Endomysium IgA Ab [Titer] in Serum

0.00

0.20

0.0

1.0

—

(3046870) Tissue transglutaminase IgG Ab [Units/volume] in Serum

0.00

0.20

0.0

1.1

—

(40767503) Oxygen content in Capillary blood by calculation

0.00

0.20

0.0

2.8

—

14.2

—

(40768797) Stomach Pathology biopsy report

1.22

0.19

1.1

1.3

—

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

1.20

0.17

1.9

1.6

—

(3000494) Fungus identified in Specimen by Culture

1.07

0.10

1.2

1.4

—

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

1.06

0.09

2.2

1.6

—

(3022948) Iron [Moles/volume] in Serum or Plasma

1.09

0.08

3.7

2.5

10.2

14.4

umol/l

—

(3019050) Tissue transglutaminase IgA Ab [Units/volume] in Serum

1.08

0.08

1.1

1.2

—

0.7

—

(40760892) CBC W Ordered Manual Differential panel - Blood

1.06

0.07

6.7

5.6

—

(1761868) Lipid panel - Serum or Plasma

125

1.05

0.00

2.5

2.7

—

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

0.86

0.00

2.2

1.5

—

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

0.00

0.0

1.6

—

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

0.00

0.0

1.0

—

(3027544) Mycobacterium sp identified in Sputum by Organism specific culture

0.00

0.0

3.8

—

(3014973) Borrelia burgdorferi IgM Ab [Units/volume] in Cerebral spinal fluid

0.00

0.0

1.0

—

(3019902) Methicillin resistant Staphylococcus aureus [Presence] in Specimen by Organism specific culture

1.00

0.00

4.4

4.6

—

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

0.00

0.0

1.0

—

(3025130) Human papilloma virus identified in Specimen

0.00

0.0

2.4

—

(3032773) Endomysium IgG Ab [Titer] in Serum

0.00

0.0

1.0

—

(44816559) Phosphatidylethanol [Mass/volume] in Blood

0.00

0.0

1.0

—

(40768806) Pleura Pathology biopsy report

0.00

0.0

1.5

—

(40768795) Lymph node Pathology biopsy report

0.00

0.0

1.0

—

(3022756) Ceruloplasmin [Mass/volume] in Serum or Plasma

0.00

0.0

1.2

—

239.6

—

(3000855) Microscopic observation [Identifier] in Vaginal fluid by Gram stain

0.00

0.0

1.2

—

(3016650) Hepatitis A virus Ab [Presence] in Serum

0.00

0.0

1.0

—

(3004616) Nuclear Ab [Presence] in Serum

0.00

0.0

1.2

—

(3044242) Glucose [Moles/volume] in Arterial blood

0.00

0.0

2.0

—

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

0.00

0.0

1.0

—

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

0.00

0.0

1.0

—

(40768441) Liver Pathology biopsy report

0.00

0.0

1.0

—

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

0.00

0.0

1.3

—

(3018559) Microscopic observation [Identifier] in Buccal smear by Cyto stain

0.00

0.0

1.0

—

(3029080) Hemoglobin [Entitic mass] in Reticulocytes

0.00

0.0

1.0

—

34.8

—

(3004248) Sex hormone binding globulin [Moles/volume] in Serum or Plasma

0.00

0.0

1.8

—

39.6

—

(1617658) Protocol used for examination of sentinel lymph nodes

0.00

0.0

1.0

—

(3013327) Hepatitis A virus IgM Ab [Presence] in Serum

0.00

0.0

1.0

—

(3010380) Borrelia burgdorferi IgG Ab [Units/volume] in Cerebral spinal fluid

0.00

0.0

1.0

—

(3048821) Cortisol [Moles/volume] in Serum or Plasma --post 1 mg dexamethasone PO overnight

0.00

0.0

1.2

—

(40766189) Gliadin peptide IgG Ab [Units/volume] in Serum by Immunoassay

0.00

0.0

1.1

—

(3005570) Glucose [Moles/volume] in Urine

0.00

0.0

1.9

—

(3017569) Oxygen content in Arterial blood

0.00

0.0

2.2

—

(42529200) Cancer Ag 15-3 [Units/volume] in Serum or Plasma by Immunoassay

0.00

0.0

2.6

—

25.0

—

(40768800) Prostate Pathology biopsy report

0.00

0.0

1.1

—

(40762485) Glomerular basement membrane Ab [Units/volume] in Serum by Immunoassay

0.00

0.0

1.2

—

Mortality – FinRegistry

↥

Association

Association between endpoint CD2_BENIGN_RENALPELVIS and mortality.

Females

Parameter	HR [95% CI]	p-value
CD2_BENIGN_RENALPELVIS	2.195 [1.51, 3.2]	< 0.001
Birth year	0.995 [0.99, 1.0]	0.211

During the follow-up period (1.1.1998 — 31.12.2019), 71 out of 169 females with CD2_BENIGN_RENALPELVIS died.

Males

Parameter	HR [95% CI]	p-value
CD2_BENIGN_RENALPELVIS	2.034 [1.28, 3.22]	0.003
Birth year	0.988 [0.98, 1.0]	0.011

During the follow-up period (1.1.1998 — 31.12.2019), 64 out of 125 males with CD2_BENIGN_RENALPELVIS died.

Mortality risk

Mortality risk for people of age

years, who have CD2_BENIGN_RENALPELVIS.

N-year risk	Females	Males
1	0.193%	0.366%
5	1.243%	2.299%
10	3.296%	5.613%
15	5.789%	10.899%
20	10.092%	17.7%

Relationships between endpoints

↥

Index endpoint: CD2_BENIGN_RENALPELVIS – Benign neoplasm: Renal pelvis

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 neoplasm: Renal pelvis

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