AFAP1 p.Asn812=
c.2436C>T · rs114329356 · VCV2654639
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.879%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.31 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.1 | GERP -2.5 |
| Overall | ||
| CADD | 2.091 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.879%
European (non-Finnish) · 10,086/1,146,884 alleles
Filtering AF
0.865%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.859%
Overall
0.706%
10,954/1,551,574 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.879% | 114 |
| Remaining individualsnot grpmax-eligible | 0.557% | 179 |
| Admixed American | 0.472% | 212 |
| African / African-American | 0.145% | 690 |
| South Asian | 0.136% | 737 |
| Finnishnot grpmax-eligible | 0.107% | 936 |
| Middle Eastern | 0.1% | 998 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00698% | 14,325 |
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
- AFAP1
- Protein
- p.Asn812=
- Coding
- c.2436C>T
- MANE Select
- NM_001134647
- dbSNP
- rs114329356
- Type
- single nucleotide variant
- Location
- chr4:7763774 (GRCh38)
- Gene constraint
- LOEUF 0.918 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.09
Similar variants
- AFAP1 p.Val288Ala Uncertain significance ★★ ⚠ same type
- AFAP1 p.Ala783= Likely benign ★★ same type
- AFAP1 p.Asn686= Likely benign ★★ same type
- AFAP1 p.Glu705= Benign ★★ same type
- AFAP1 p.Ala438Ser Uncertain significance ★ ⚠ same type
- AFAP1 p.Ala534Ser Uncertain significance ★ same type
- AFAP1 p.Ala587Val Uncertain significance ★ same type
- AFAP1 p.Ala624Val Uncertain significance ★ ⚠ 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/afap1-p-asn812 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown