VIL1 p.Ala673=
c.2019C>T · rs34509505 · VCV785992
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.7%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -4.4 |
| Overall | ||
| CADD | 0.123 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.7%
African / African-American · 1,272/75,022 alleles
Filtering AF
1.62%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.59%
Overall
0.103%
1,663/1,614,122 alleles · low-frequency
exomes 930/1,461,878 · genomes 733/152,244 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.7% | 59 |
| Middle Eastern | 0.643% | 155 |
| Remaining individualsnot grpmax-eligible | 0.163% | 613 |
| Admixed American | 0.157% | 638 |
| East Asian | 0.0178% | 5,610 |
| South Asian | 0.0143% | 7,006 |
| European (non-Finnish) | 0.0114% | 8,741 |
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
- VIL1
- Protein
- p.Ala673=
- Coding
- c.2019C>T
- MANE Select
- NM_007127
- dbSNP
- rs34509505
- Type
- single nucleotide variant
- Location
- chr2:218437171 (GRCh38)
- Gene constraint
- LOEUF 0.946 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.98 · 2 PDB
- Residue 673
- an α-helix; the 'core' region
Similar variants
- VIL1 p.Ala673Val Uncertain significance ★ ⚠ same residue
- VIL1 p.Arg505Gln Uncertain significance ★★ ⚠ same type
- VIL1 p.Arg630Cys Benign ★★ same type
- VIL1 p.Asn593Lys Benign ★★ same type
- VIL1 p.His228Gln Likely benign ★★ same type
- VIL1 p.Val258Leu Benign ★★ same type
- VIL1 p.Ala123Val Uncertain significance ★ ⚠ same type
- VIL1 p.Ala218Ser 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/vil1-p-ala673 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown