Benign neoplasm: Urethra

CD2_BENIGN_URETHRA_EXALLC

No definition available.

Endpoint definition

↥

Endpoint definition steps	FinnGen
Phenotype data
1. Apply sex-specific rule None	-
2. Check conditions None
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Hospital discharge: ICD-10 — D30.4& Hospital discharge: ICD-9 — 2232 Cause of death: ICD-10 — D30.4& Cause of death: ICD-9 — 2232 2 out of 7 registries used, show all original rules.	-
4. Check minimum number of events None	-
5. Include endpoints None	-
6. Filter based on genotype QC (FinnGen only) None	-

Control definitions (FinnGen only)

Control exclude: C3_CANCER, C3_CANCER_WIDE

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 urethrae

NAME	CD2_BENIGN_URETHRA_EXALLC
CONTROL_EXCLUDE	C3_CANCER\|C3_CANCER_WIDE
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	D304
HD_ICD_9	2232
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	D304
COD_ICD_9	2232
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 neoplasm: Urethra based on the number of shared cases.

Similar with more cases:

Similar with less cases:

Benign neoplasm: Urethra

Case counts by codes

↥

FinnGen case counts by registry codes:

No upset plot: script not run.

No upset table: script not run.

Summary Statistics

↥

-FinRegistry-

This endpoint is excluded from FinRegistry analyses (omitted endpoint).

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	46	29	17
Unadjusted period prevalence (%)	0.01	0.01	0.01
Median age at first event (years)	60.55	59.01	63.17

-FinnGen-

Age distribution of first events

-FinnGen-

Year distribution of first events

-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

(3049717) Cytology report of Urine Cyto stain

11.73

9.37

3.8

2.0

—

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

9.62

3.36

1.5

2.4

—

(40761535) Cells panel - Urine sediment

3.82

3.17

3.7

3.5

—

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

253

3.36

3.06

8.6

4.2

—

716.6

—

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

138

2.55

2.44

4.5

2.9

—

(3002256) Pathology report gross observation

3.60

2.38

1.2

1.1

—

(3029937) Albumin [Presence] in Urine by Test strip

2.48

2.10

5.4

4.2

0.0

estimate

—

(3037467) Urinalysis macro (dipstick) panel - Urine

265

2.65

1.98

7.1

4.0

—

(3003510) Neisseria gonorrhoeae DNA [Presence] in Urine by NAA with probe detection

3.56

1.97

2.1

1.7

—

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

168

2.26

1.91

5.2

3.4

—

(40768804) Tissue Pathology biopsy report

118

2.23

1.80

2.6

1.6

—

(3021347) Calcium.ionized [Moles/volume] in Serum or Plasma

162

2.19

1.79

8.2

4.3

1.2

mmol/l

0.40

146

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

2.69

1.74

9.5

8.0

—

(3024950) Chlamydia trachomatis DNA [Presence] in Urine by NAA with probe detection

3.11

1.73

2.6

1.6

—

(3035350) Ketones [Presence] in Urine by Test strip

193

2.15

1.68

4.3

3.2

0.0

estimate

—

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

194

2.13

1.65

5.1

3.4

10.4

10.9

umol/l

0.20

178

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

176

2.10

1.62

8.0

4.7

1.2

mmol/l

0.14

154

(3045414) Leukocytes [Presence] in Urine

3.60

1.56

1.8

1.7

—

(3026008) Bacteria identified in Urine by Culture

118

2.04

1.45

5.5

3.0

—

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

145

1.99

1.42

4.4

3.4

—

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

2.35

1.40

1.6

1.7

—

(3042936) Bacteria identified in Isolate by Culture

2.38

1.40

1.7

2.2

—

(3023368) Bacteria identified in Blood by Culture

2.05

1.31

3.9

3.8

—

(3021601) Nitrite [Presence] in Urine by Test strip

197

1.90

1.25

4.7

4.4

0.0

estimate

—

(3048689) Calprotectin [Mass/mass] in Stool

2.27

1.22

2.8

1.7

100.9

89.4

ug/g

—

(3015736) pH of Urine

151

1.88

1.22

3.6

3.3

—

(3009261) Glucose [Presence] in Urine by Test strip

198

1.88

1.22

4.3

3.3

0.0

estimate

—

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

2.18

1.12

1.3

—

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

1.91

1.11

2.9

3.4

—

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

2.24

1.08

1.9

1.7

—

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

2.24

1.08

1.4

1.6

—

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

2.04

1.06

2.0

1.4

—

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

2.18

1.05

1.4

1.6

—

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

2.31

0.95

1.7

1.3

—

(3019060) Gas panel - Arterial blood

2.22

0.93

4.0

3.5

—

(3044640) Blood type and Crossmatch panel - Blood

1.76

0.90

2.1

2.0

—

(3019225) pH of Specimen

1.94

0.82

6.2

2.5

—

(1761868) Lipid panel - Serum or Plasma

137

0.57

0.76

2.7

3.3

—

(36304419) Bacteria [Presence] in Urine

105

1.64

0.72

4.4

2.6

—

(3048816) Calcium.ionized [Moles/volume] adjusted to pH 7.4 in Blood

1.88

0.68

5.0

2.3

1.3

1.2

mmol/l

—

(3023520) Reticulocytes [#/volume] in Blood

1.75

0.63

1.4

3.0

47.6

64.1

e9/l

—

(3001019) Free T4 and TSH panel - Serum or Plasma

0.00

0.62

0.0

1.1

—

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

155

1.51

0.61

2.6

3.7

16.8

45.1

ng/l

1.24

107

(3022145) Colonoscopy Study observation

1.76

0.59

1.5

1.3

—

(3002385) Erythrocyte distribution width [Ratio]

322

0.67

0.57

27.7

14.7

13.5

0.11

316

(42870588) Differential panel, method unspecified - Blood

120

1.51

0.56

2.1

4.9

—

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

1.57

0.54

1.0

1.6

—

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

1.54

0.49

1.0

1.6

—

(3002582) Erythrocytes [#/volume] in Urine

123

1.46

0.49

4.9

2.9

29.1

535.5

e6/l

0.47

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

1.54

0.48

2.2

1.9

—

(40758558) Short blood count panel - Blood

1.52

0.46

2.3

5.1

—

(3013603) Prostate specific Ag [Mass/volume] in Serum or Plasma

1.46

0.43

6.9

4.2

2.6

2.2

ug/l

0.21

(3016293) Bicarbonate [Moles/volume] in Serum or Plasma

0.00

0.42

0.0

4.9

—

25.9

—

(3050449) Albumin [Mass/time] in Urine collected for unspecified duration

0.00

0.41

0.0

2.4

—

15.8

—

(3024889) Methemoglobin/Hemoglobin.total in Venous blood

0.00

0.41

0.0

2.8

—

0.6

—

(3010517) Carboxyhemoglobin/Hemoglobin.total in Venous blood

0.00

0.41

0.0

2.8

—

0.7

—

(3007853) Bacteria identified in Skin by Aerobe culture

1.53

0.38

1.3

1.6

—

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

409

0.70

0.33

22.6

14.4

139.0

139.7

mmol/l

0.85

397

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

112

1.36

0.33

4.6

2.6

0.1

0.5

e6/l

1.08

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

408

0.71

0.33

22.9

14.5

4.0

mmol/l

1.37

397

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

375

0.72

0.31

15.3

10.7

74.4

77.8

ml/min/173m2

0.44

299

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

1.25

0.27

2.9

2.3

2.5

2.4

mmol/l

—

(3021337) Troponin I.cardiac [Mass/volume] in Serum or Plasma

0.71

0.27

4.2

3.3

24.5

94.6

ng/l

—

(3044889) 12 lead EKG panel

275

0.80

0.24

5.1

3.6

—

(3048929) Epstein Barr virus Ab [Presence] in Serum

0.00

0.21

0.0

1.0

—

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

0.00

0.21

0.0

2.6

—

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

0.00

0.21

0.0

1.2

—

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

0.00

0.21

0.0

1.6

—

2.7

—

(40758310) Human epididymis protein 4 [Moles/volume] in Serum or Plasma

0.00

0.21

0.0

1.5

—

58.8

—

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

0.00

0.21

0.0

1.5

—

43.0

—

(3008898) HLA-B27 [Presence]

0.00

0.21

0.0

1.1

—

(3007566) Smooth muscle Ab [Titer] in Serum

0.00

0.21

0.0

1.0

—

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

0.00

0.21

0.0

1.5

—

0.3

—

(3019150) Specific gravity of Urine by Refractometry

1.30

0.21

3.6

3.8

—

1.0

—

(4094501)

0.00

0.20

0.0

1.0

—

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

1.20

0.20

3.2

2.6

13.6

14.1

umol/l

—

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

1.20

0.19

1.6

1.8

—

(3005013) Prostate Specific Ag Free [Mass/volume] in Serum or Plasma

1.17

0.18

4.3

2.9

0.6

0.8

ug/l

—

(3020460) C reactive protein [Mass/volume] in Serum or Plasma

392

1.42

0.18

19.0

11.6

29.7

21.6

mg/l

0.48

292

(40760892) CBC W Ordered Manual Differential panel - Blood

0.79

0.16

7.1

3.4

—

(3041096) Erythrocytes [Presence] in Urine by Automated

105

1.19

0.12

5.3

2.9

—

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

215

0.88

0.10

3.1

2.7

—

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

398

1.28

0.09

5.6

4.5

5.6

6.0

mmol/l

1.67

369

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

307

1.14

0.08

5.1

4.1

15.3

14.9

pmol/l

0.28

279

(3004410) Hemoglobin A1c/Hemoglobin.total in Blood

374

0.95

0.07

6.5

5.7

37.6

40.0

mmol/mol

1.91

355

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

162

0.89

0.07

2.9

1.9

82.5

99.5

pmol/l

—

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

1.15

0.07

1.2

—

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

116

0.93

0.01

5.8

2.6

29.7

28.7

u/l

0.11

107

(3009542) Hematocrit [Volume Fraction] of Blood

348

1.02

0.00

21.4

13.4

39.7

40.5

0.29

249

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

0.00

0.0

1.3

—

(3016914) Bacteria identified in Cerebral spinal fluid by Culture

0.00

0.0

1.3

—

(3023150) Myeloperoxidase Ab [Units/volume] in Serum

0.00

0.0

2.4

—

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

0.00

0.0

1.4

—

(40766048) U1 small nuclear ribonucleoprotein 70kD Ab [Units/volume] in Serum by Immunoassay

0.00

0.0

1.0

—

(3005033) Fetal Nuchal fold Thickness US

0.00

0.0

1.7

—

(3020287) Protein C actual/normal in Platelet poor plasma by Coagulation assay

0.00

0.0

1.4

—

121.6

—

(3043238) Trisomy 21 risk [Likelihood] in Fetus

0.00

0.0

1.8

—

(3009214) Lutropin [Units/volume] in Serum or Plasma

0.00

0.0

1.0

—

12.3

—

(3013290) Carbon dioxide [Partial pressure] in Blood

0.00

0.0

1.3

—

4.9

—

(1616796) Gas panel - Central venous blood

0.00

0.0

1.8

—

(3026179) Normetanephrine [Moles/volume] in Serum or Plasma

0.00

0.0

1.2

—

0.5

—

(3003740) Influenza virus B Ag [Presence] in Specimen

0.00

0.0

1.0

—

(3049207) Fetal Trisomy 21 risk [Likelihood] Based on maternal age

0.00

0.0

1.7

—

(3016879) Cocaine [Presence] in Urine

0.00

0.0

1.3

—

(3004616) Nuclear Ab [Presence] in Serum

0.00

0.0

1.0

—

(36032269) Testosterone Free [Moles/volume] in Serum or Plasma by calculation

0.00

0.0

1.8

—

177.3

—

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

0.00

0.0

1.4

—

5.4

—

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

0.00

0.0

3.0

—

107.3

—

(44816559) Phosphatidylethanol [Mass/volume] in Blood

0.00

0.0

1.0

—

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

0.00

0.0

3.0

—

(3019230) Fractional oxyhemoglobin in Venous blood

0.00

0.0

4.0

—

59.6

—

(3032035) Polymorphonuclear cells/100 leukocytes in Blood

0.00

0.0

4.4

—

66.6

—

(3030366) Cystatin C [Mass/volume] in Serum or Plasma

0.00

0.0

1.2

—

1.2

—

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

0.00

0.0

1.1

—

(46235831) Pregnancy associated plasma protein A [Multiple of the median] adjusted in Serum or Plasma

0.00

0.0

1.7

—

(3027008) Opiates [Presence] in Urine

0.00

0.0

1.3

—

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

0.00

0.0

3.0

—

4.0

—

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

0.00

0.0

1.2

—

(3026389) Candida sp identified in Specimen by Organism specific culture

0.00

0.0

1.3

—

(3000764) Benzodiazepines [Presence] in Urine

0.00

0.0

1.3

—

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

0.00

0.0

1.0

—

(3027456) Digoxin [Moles/volume] in Serum or Plasma

0.00

0.0

4.2

—

0.8

—

(3025130) Human papilloma virus identified in Specimen

0.00

0.0

2.0

—

(43055120) Cytomegalovirus DNA [Units/volume] (viral load) in Serum or Plasma by NAA with probe detection

0.00

0.0

1.0

—

(40763531) Fetal Nuchal fold [Multiple of the median] Thickness adjusted for maternal weight

0.00

0.0

1.7

—

(3028300) Cannabinoids [Presence] in Urine

0.00

0.0

1.3

—

(3011288) Drugs identified in Urine by Screen method

0.00

0.0

2.0

—

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

0.00

0.0

1.0

—

(3013512) EKG study

120

1.00

0.00

3.7

3.6

—

(3042111) Morphology [Interpretation] in Bone marrow Narrative

0.00

0.0

2.2

—

(3032836) C peptide [Moles/volume] in Serum or Plasma --fasting

0.00

0.0

1.0

—

0.8

—

(3021387) Prolactin [Units/volume] in Serum or Plasma

0.00

0.0

1.5

—

352.8

—

(3021788) Differential panel - Synovial fluid

0.00

0.0

1.0

—

(3021901) Oxygen saturation in Capillary blood

0.00

0.0

1.3

—

(3027944) Amphetamines [Presence] in Urine

0.00

0.0

1.3

—

(3008714) Choriogonadotropin [Multiple of the median] adjusted in Serum or Plasma

0.00

0.0

1.7

—

(3002523) Influenza virus A Ag [Presence] in Specimen

0.00

0.0

1.0

—

(3047352) Trisomy 18 risk [Likelihood] in Fetus

0.00

0.0

1.7

—

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

0.00

0.0

1.1

—

(3030408) 3-Methoxytyramine [Moles/volume] in Serum or Plasma

0.00

0.0

1.2

—

(3009340) Metanephrine [Moles/volume] in Serum or Plasma

0.00

0.0

1.0

—

(3019145) Choriogonadotropin.beta subunit free [Mass/volume] in Serum or Plasma

0.00

0.0

1.7

—

(3041145) Herpes simplex virus IgM Ab [Presence] in Serum by Immunoassay

0.00

0.0

1.0

—

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

0.00

0.0

1.4

—

(3027315) Oxygen [Partial pressure] in Blood

0.00

0.0

1.3

—

7.7

—

Mortality – FinRegistry

↥

This endpoint is excluded from FinRegistry analyses (omitted endpoint).

Relationships between endpoints

↥

Index endpoint: CD2_BENIGN_URETHRA_EXALLC – Benign neoplasm: Urethra

GWS hits: -

This endpoint is excluded from FinRegistry analyses (omitted endpoint).

≡ Risteys

FG R12 + FR

FinnGen R11 + FinRegistry

FinnGen R10 + FinRegistry

FinnGen R10

FinnGen R9

FinnGen R8

FinnGen R7

FinnGen R6

FinnGen R5

FinnGen R4

FinnGen R3

Benign neoplasm: Urethra

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)

All original rules

Similar endpoints

Case counts by codes

Summary Statistics

-FinRegistry-

-FinnGen-

Key figures

-FinnGen-

Age distribution of first events

-FinnGen-

Year distribution of first events

-FinnGen-

Cumulative Incidence Function

CodeWAS (R11)

LabWAS

Mortality – FinRegistry

Relationships between endpoints