Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.389%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.58 | GERP -4.4 |
| Overall | ||
| CADD | 1.425 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.389%
South Asian · 354/91,086 alleles
Filtering AF
0.355%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.342%
Overall
0.0502%
810/1,614,224 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.389% | 257 |
| Middle Eastern | 0.281% | 356 |
| Admixed American | 0.143% | 698 |
| Remaining individualsnot grpmax-eligible | 0.0672% | 1,488 |
| Finnishnot grpmax-eligible | 0.0531% | 1,884 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0507% | 1,974 |
| European (non-Finnish) | 0.022% | 4,539 |
| African / African-American | 0.00266% | 37,524 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- ANPEP
- Protein
- p.Ser613=
- Coding
- c.1839C>T
- MANE Select
- NM_001150
- dbSNP
- rs1143654
- Type
- single nucleotide variant
- Location
- chr15:89799540 (GRCh38)
- Gene constraint
- LOEUF 0.705 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.55 · 15 PDB
- Residue 613
- the 'metalloprotease' region
Similar variants
- ANPEP c.1437+8C>G Benign ★★ same type
- ANPEP c.1437+9C>G Benign ★★ same type
- ANPEP p.Ala311Val Benign ★★ ⚠ same type
- ANPEP p.Ala422Gly Likely benign ★★ ⚠ same type
- ANPEP p.Ala671= Benign ★★ same type
- ANPEP p.Glu770= Benign ★★ same type
- ANPEP p.Leu100= Benign/Likely benign ★★ same type
- ANPEP p.Leu258Ile Likely benign ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/anpep-p-ser613 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown