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Early syphilis

EFO Endpoint Browser PheWeb

AB1_EARLY_SYPHILIS

Endpoint definition

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Endpoint definition steps

FinnGen

Phenotype data

473681

1. Apply sex-specific rule

None

473681

2. Check conditions

None

473681

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

Registry filters:

  • Hospital discharge: ICD-10 — A51
  • Hospital discharge: ICD-9 — 09[1]
  • Hospital discharge: ICD-8 — 09[1]
  • Cause of death: ICD-10 — A51
  • Cause of death: ICD-9 — 09[1]
  • Cause of death: ICD-8 — 09[1]

2 out of 7 registries used, show all original rules.

376

4. Check minimum number of events

None

376

5. Include endpoints

None

376

6. Filter based on genotype QC (FinnGen only)

344

Control definitions (FinnGen only)

Control exclude AB1_SEXUAL_TRANSMISSION

Extra metadata

Level in the ICD hierarchy 4
First used in FinnGen datafreeze DF5

Case counts by codes

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FinnGen case counts by registry codes:

generic upset plot

Upset plot

Full data table

Summary Statistics

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-FinRegistry-

Key figures

All Female Male
Number of individuals
Whole population 2515 815 1643
Only index persons 2222 742 1480
Unadjusted period prevalence (%)
Whole population 0.04 0.02 0.05
Only index persons 0.05 0.03 0.06
Median age at first event (years)
Whole population 36.88 33.67 38.63
Only index persons 36.48 32.83 38.31

-FinnGen-

Key figures

All Female Male
Number of individuals 344 82 262
Unadjusted period prevalence (%) 0.11 0.03 0.13
Median age at first event (years) 39.42 31.45 41.92

-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

No data

Mortality – FinRegistry

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Association

Association between endpoint AB1_EARLY_SYPHILIS and mortality.

Females

No data

Males

Parameter HR [95% CI] p-value
AB1_EARLY_SYPHILIS 1.498 [1.19, 1.88] < 0.001
Birth year 0.983 [0.97, 0.99] 0.001

During the follow-up period (1.1.1998 — 31.12.2019), 80 out of 997 males with AB1_EARLY_SYPHILIS died.

Mortality risk

Mortality risk for people of age

years, who have AB1_EARLY_SYPHILIS.

N-year risk Females Males
1 No data 0.299%
5 No data 1.658%
10 No data 4.176%
15 No data 7.743%
20 No data 12.609%

Relationships between endpoints

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Index endpoint: AB1_EARLY_SYPHILIS – Early syphilis

GWS hits: -

Endpoint
Case Overlap
Survival Analysis
Genetic Correlations
Genetic Signals
N (Jaccard index)
HR [CI]
Extremity
rg [CI]
Extremity
Hits
Coloc Hits
FinRegistry
FinnGen
FinRegistry
FinnGen
FinnGen
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