Benign lipomatous neoplasm of spermatic cord

CD2_BENIGN_LIPO_SPERMATIC

adrenal gland neoplasm: A neoplasm (disease) that involves the adrenal gland.

Endpoint definition

↥

Endpoint definition steps	FinnGen
Phenotype data	520210
1. Apply sex-specific rule only males	226837
2. Check conditions None	226837
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Hospital discharge: ICD-10 — D17.6& Cause of death: ICD-10 — D17.6& 2 out of 7 registries used, show all original rules.	48
4. Check minimum number of events None	48
5. Include endpoints None	48
6. Filter based on genotype QC (FinnGen only)	48

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 funiculi spermatici

NAME	CD2_BENIGN_LIPO_SPERMATIC
CONTROL_EXCLUDE
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX	1
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	D176
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	D176
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 spermatic cord based on the number of shared cases.

Similar with more cases:

Similar with less cases:

Benign lipomatous neoplasm of spermatic cord

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	543	-	543
Only index persons	497	-	497
Unadjusted period prevalence (%)
Whole population	0.02	-	0.02
Only index persons	0.02	-	0.02
Median age at first event (years)
Whole population	-	-	57.75
Only index persons	-	-	56.61

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	48	-	48
Unadjusted period prevalence (%)	0.02	-	0.02
Median age at first event (years)	54.27	-	54.27

-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

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

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

4.11

5.34

3.0

3.4

—

(40761535) Cells panel - Urine sediment

5.91

5.31

2.9

3.5

—

(3044640) Blood type and Crossmatch panel - Blood

109

3.13

3.62

3.2

3.4

—

(3019060) Gas panel - Arterial blood

4.42

3.56

12.9

4.4

—

(3002385) Erythrocyte distribution width [Ratio]

297

0.34

3.18

38.5

18.5

13.7

0.05

289

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

2.87

2.78

5.0

2.9

—

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

156

2.67

2.77

7.3

4.7

—

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

3.25

2.37

2.8

1.4

—

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

2.81

2.29

3.1

1.7

—

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

6.05

2.27

1.4

1.2

—

(3016251) Hemoglobin.gastrointestinal [Presence] in Stool

4.12

2.24

2.0

2.1

—

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

3.06

2.17

2.8

1.5

—

(3023368) Bacteria identified in Blood by Culture

108

2.26

1.86

7.4

4.5

—

(3019150) Specific gravity of Urine by Refractometry

2.30

1.65

5.9

3.1

—

1.0

—

(3026008) Bacteria identified in Urine by Culture

2.26

1.59

5.2

2.7

—

(3022145) Colonoscopy Study observation

2.47

1.47

1.2

—

(40768797) Stomach Pathology biopsy report

2.42

1.45

1.6

1.2

—

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

2.71

1.35

1.2

1.5

—

(3051552) Clostridioides difficile toxin genes [Presence] in Stool by NAA with probe detection

2.59

1.28

1.8

1.6

—

(3007853) Bacteria identified in Skin by Aerobe culture

2.23

1.13

3.0

2.0

—

(3007220) Creatine kinase [Enzymatic activity/volume] in Serum or Plasma

110

1.84

1.10

2.7

2.1

189.6

382.9

u/l

0.55

101

(3006140) Bilirubin.total [Moles/volume] in Serum or Plasma

185

1.73

1.03

7.9

7.7

9.5

12.1

umol/l

0.91

178

(3009542) Hematocrit [Volume Fraction] of Blood

331

0.58

0.99

25.9

15.2

40.2

40.8

0.07

233

(3037522) Nuclear Ab [Titer] in Serum

2.30

0.95

1.2

1.5

—

371.4

—

(40760892) CBC W Ordered Manual Differential panel - Blood

1.83

0.93

6.5

4.9

—

(3041096) Erythrocytes [Presence] in Urine by Automated

109

0.49

0.85

4.2

2.9

—

(3036481) Cortisol [Moles/volume] in Serum or Plasma

2.00

0.85

1.3

1.6

313.5

384.4

nmol/l

—

(1761868) Lipid panel - Serum or Plasma

139

0.57

0.75

2.9

3.0

—

(3015736) pH of Urine

132

1.58

0.71

5.2

2.9

—

(3003785) Carcinoembryonic Ag [Mass/volume] in Serum or Plasma

1.69

0.68

2.4

4.7

3.4

7.9

ug/l

—

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

145

1.51

0.62

5.5

3.3

—

(3018677) aPTT in Platelet poor plasma by Coagulation assay

1.50

0.55

1.3

2.1

27.8

29.2

—

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

1.57

0.50

3.9

7.2

—

(3042936) Bacteria identified in Isolate by Culture

1.54

0.46

2.5

2.0

—

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

1.46

0.43

1.7

1.3

—

(3000330) Specific gravity of Urine by Test strip

0.00

0.40

0.0

4.4

—

(3044889) 12 lead EKG panel

266

0.74

0.40

4.8

4.3

—

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

1.43

0.39

4.2

1.8

—

(3013721) Aspartate aminotransferase [Enzymatic activity/volume] in Serum or Plasma

109

0.68

0.33

4.8

3.4

25.5

37.0

u/l

—

103

(3017446) Testosterone [Moles/volume] in Serum or Plasma

0.65

0.28

2.6

2.2

13.6

13.0

nmol/l

—

(3021960) Folate [Moles/volume] in Serum or Plasma

1.33

0.28

1.6

1.5

15.9

18.5

nmol/l

—

(3016431) Calcium.ionized [Moles/volume] adjusted to pH 7.4 in Serum or Plasma

164

1.26

0.26

23.8

8.1

1.2

mmol/l

0.26

138

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

1.35

0.24

4.6

2.0

—

(4035726)

1.31

0.24

1.0

1.4

—

(3002256) Pathology report gross observation

1.31

0.24

1.2

1.3

—

(3013512) EKG study

122

0.77

0.22

5.1

4.7

—

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

1.21

0.22

1.4

1.1

—

32.0

—

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

0.00

0.21

0.0

5.9

—

1.6

—

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

0.00

0.21

0.0

6.4

—

8.9

—

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

0.00

0.21

0.0

2.8

—

(3027008) Opiates [Presence] in Urine

0.00

0.21

0.0

1.2

—

(3028300) Cannabinoids [Presence] in Urine

0.00

0.21

0.0

1.2

—

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

0.00

0.21

0.0

1.1

—

(3027944) Amphetamines [Presence] in Urine

0.00

0.21

0.0

1.2

—

(3016879) Cocaine [Presence] in Urine

0.00

0.21

0.0

1.2

—

(3000764) Benzodiazepines [Presence] in Urine

0.00

0.21

0.0

1.2

—

(4094501)

0.00

0.21

0.0

1.3

—

(3037467) Urinalysis macro (dipstick) panel - Urine

244

0.82

0.21

7.0

3.7

—

(44816559) Phosphatidylethanol [Mass/volume] in Blood

0.00

0.21

0.0

1.2

—

(3036489) Thrombin time

0.00

0.21

0.0

2.0

—

27.2

—

(3037121) Protein [Mass/volume] in Urine

0.00

0.21

0.0

3.6

—

0.2

—

(3026493) Urate [Moles/volume] in Serum or Plasma

119

1.25

0.21

5.4

2.9

367.1

7763.9

umol/l

0.79

(3037756) Immunofixation for Serum or Plasma

0.00

0.20

0.0

1.5

—

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

0.00

0.20

0.0

5.0

—

(40760888) Immunoglobulin light chains.free panel - Serum

0.00

0.20

0.0

4.4

—

(3000515) Antithrombin actual/normal in Platelet poor plasma by Chromogenic method

0.00

0.20

0.0

1.6

—

77.4

—

(3020059) Calcium [Moles/volume] corrected for albumin in Serum or Plasma

1.24

0.19

1.3

3.1

2.4

mmol/l

—

(3023103) Potassium [Moles/volume] in Serum or Plasma

398

0.78

0.19

32.9

16.8

4.2

4.0

mmol/l

1.53

387

(42870588) Differential panel, method unspecified - Blood

117

0.82

0.15

11.9

6.8

—

(40761511) CBC panel - Blood by Automated count

386

0.82

0.14

21.0

15.6

—

(3019550) Sodium [Moles/volume] in Serum or Plasma

395

0.82

0.13

33.3

16.8

139.6

139.4

mmol/l

0.28

384

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

1.18

0.10

4.2

4.0

—

(3000963) Hemoglobin [Mass/volume] in Blood

424

0.92

0.09

38.0

21.7

137.6

140.1

g/l

0.42

415

(3035941) MCH [Entitic mass]

424

0.92

0.09

37.8

21.4

30.0

30.7

1.43

415

(3026361) Erythrocytes [#/volume] in Blood

424

0.92

0.09

37.9

21.5

4.6

e12/l

0.11

407

(3024731) MCV [Entitic volume]

424

0.92

0.09

37.8

21.5

90.5

91.7

0.64

415

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

413

0.95

0.08

28.9

17.9

116.2

88.7

umol/l

0.94

413

(3051714) Fibrin D-dimer FEU [Mass/volume] in Platelet poor plasma

0.84

0.08

1.0

1.7

0.3

2.0

mg/l

—

(3035995) Alkaline phosphatase [Enzymatic activity/volume] in Serum or Plasma

292

0.90

0.07

10.9

7.9

68.0

74.6

u/l

1.01

279

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

369

1.14

0.07

4.4

5.1

6.0

6.1

mmol/l

0.19

337

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

183

0.97

0.00

3.6

2.2

—

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

145

1.05

0.00

3.0

2.7

—

(3001784) Prostate Specific Ag Free/Prostate specific Ag.total in Serum or Plasma

246

1.03

0.00

3.6

4.4

24.3

20.8

0.87

129

(36304419) Bacteria [Presence] in Urine

108

1.02

0.00

3.3

2.4

—

(40768804) Tissue Pathology biopsy report

138

1.02

0.00

1.6

2.0

—

(40768806) Pleura Pathology biopsy report

0.00

0.0

1.3

—

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

0.00

0.0

4.6

—

4.2

—

(3008757) Leukocyte morphology finding [Identifier] in Blood

0.00

0.0

4.3

—

(3038546) Human coronavirus OC43 RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

3.2

—

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

1.02

0.00

5.6

1.8

—

(3052851) Hemolysis interference index of Serum or Plasma

0.00

0.0

5.7

—

(37020957) Sapovirus genogroups I+II+IV+V RNA [Presence] in Stool by NAA with probe detection

0.00

0.0

2.0

—

(3005988) Vibrio sp identified in Specimen by Organism specific culture

0.00

0.0

2.5

—

(3018387) Mycoplasma pneumoniae IgG Ab [Units/volume] in Serum

0.00

0.0

1.2

—

(3035637) Corticotropin [Mass/volume] in Plasma

0.00

0.0

1.2

—

(40757349) CD3+CD4+ (T4 helper) cells/CD3+CD8+ (T8 suppressor cells) cells [# Ratio] in Blood

0.00

0.0

1.8

—

(36033641) SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Rapid immunoassay

0.00

0.0

1.0

—

(37021247) Adenovirus 40+41 DNA [Presence] in Stool by NAA with probe detection

0.00

0.0

2.0

—

(3044927) Protein electrophoresis panel - Urine

0.00

0.0

1.6

—

(3025468) Yersinia sp identified in Specimen by Organism specific culture

0.00

0.0

2.8

—

(3012441) Differential panel - Pleural fluid

0.00

0.0

1.3

—

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

0.00

0.0

1.2

—

(40768795) Lymph node Pathology biopsy report

0.00

0.0

1.0

—

(3040359) Human coronavirus NL63 RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

3.2

—

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

0.00

0.0

4.6

—

(3024522) Salmonella sp identified in Specimen by Organism specific culture

0.00

0.0

2.8

—

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

0.00

0.0

1.3

—

(3009595) Pneumocystis jiroveci DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.6

—

(3011288) Drugs identified in Urine by Screen method

0.00

0.0

1.2

—

(3000494) Fungus identified in Specimen by Culture

0.96

0.00

1.0

1.6

—

(40758558) Short blood count panel - Blood

0.96

0.00

16.9

7.3

—

(37020445) Astrovirus RNA [Presence] in Stool by NAA with probe detection

0.00

0.0

2.0

—

(21493466) Plesiomonas shigelloides DNA [Presence] in Stool by NAA with non-probe detection

0.00

0.0

2.5

—

(3017354) Segmented neutrophils/100 leukocytes in Blood

0.00

0.0

4.1

—

55.4

—

(42868716) Shigella species+EIEC invasion plasmid antigen H ipaH gene [Presence] in Stool by NAA with probe detection

0.00

0.0

2.8

—

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

0.00

0.0

1.2

—

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

0.00

0.0

1.2

—

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

0.00

0.0

1.2

—

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

0.00

0.0

1.8

—

(3010566) Parathyrin.intact [Moles/volume] in Serum or Plasma

0.00

0.0

3.1

—

(3041642) Human coronavirus 229E RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

3.2

—

(3052649) Adenosine deaminase [Enzymatic activity/volume] in Serum or Plasma

0.00

0.0

1.4

—

14.4

—

(3021125) Hepatitis C virus RNA [Presence] in Serum or Plasma by NAA with probe detection

0.00

0.0

1.8

—

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

0.00

0.0

1.3

—

0.3

—

(3012568) Campylobacter sp identified in Specimen by Organism specific culture

0.00

0.0

2.8

—

(3029080) Hemoglobin [Entitic mass] in Reticulocytes

0.00

0.0

1.7

—

34.1

—

(42869457) Rotavirus RNA [Identifier] in Stool by NAA with probe detection

0.00

0.0

2.0

—

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

0.00

0.0

4.6

—

105.1

—

(3006923) Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma

407

1.05

0.00

13.1

10.6

28.7

28.0

u/l

0.11

393

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

0.00

0.0

1.4

—

1.3

—

(3004809) Band form neutrophils/100 leukocytes in Blood

0.00

0.0

3.7

—

0.3

—

(3014791) Apolipoprotein B [Mass/volume] in Serum or Plasma

0.00

0.0

1.4

—

0.9

—

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

0.00

0.0

1.2

—

Mortality – FinRegistry

↥

Association

Association between endpoint CD2_BENIGN_LIPO_SPERMATIC and mortality.

Females

No data

Males

Parameter	HR [95% CI]	p-value
CD2_BENIGN_LIPO_SPERMATIC	0.961 [0.81, 1.14]	0.64
Birth year	0.985 [0.98, 1.0]	0.003

During the follow-up period (1.1.1998 — 31.12.2019), 145 out of 504 males with CD2_BENIGN_LIPO_SPERMATIC died.

Mortality risk

Mortality risk for people of age

years, who have CD2_BENIGN_LIPO_SPERMATIC.

N-year risk	Females	Males
1	No data	0.174%
5	No data	1.045%
10	No data	2.736%
15	No data	4.963%
20	No data	8.282%

Relationships between endpoints

↥

Index endpoint: CD2_BENIGN_LIPO_SPERMATIC – Benign lipomatous neoplasm of spermatic cord

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 spermatic cord

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