FRAS1 p.Ala1626Val
c.4877C>T · rs17003213 · VCV697981
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.55%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.048 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.6 | GERP -5.4 |
| Regional constraint | o/e 0.97 | unconstrained · MANE · 483 kb · p 0.045 · regional, not allelic |
| Overall | ||
| CADD | 2.814 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.55%
African / African-American · 1,160/75,026 alleles
Filtering AF
1.47%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.44%
Overall
0.0794%
1,281/1,613,850 alleles · low-frequency
exomes 633/1,461,624 · genomes 648/152,226 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.55% | 65 |
| Remaining individualsnot grpmax-eligible | 0.0784% | 1,275 |
| Admixed American | 0.0617% | 1,622 |
| East Asian | 0.0268% | 3,738 |
| Middle Eastern | 0.0165% | 6,060 |
| European (non-Finnish) | 0.00186% | 53,629 |
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
- FRAS1
- Protein
- p.Ala1626Val
- Coding
- c.4877C>T
- MANE Select
- NM_025074
- dbSNP
- rs17003213
- Type
- single nucleotide variant
- Location
- chr4:78430325 (GRCh38)
- Gene constraint
- LOEUF 0.729 · pLI <0.01 (gnomAD)
- Residue 1626
- a UniProt-annotated variant site (in)
Similar variants
- FRAS1 p.Ala1626= Likely benign ★ same residue
- FRAS1 c.1072-1G>C Likely pathogenic ★★ same type
- FRAS1 c.11298+1G>A Pathogenic/Likely pathogenic ★★ same type
- FRAS1 c.2722+1G>A Pathogenic/Likely pathogenic ★★ same type
- FRAS1 c.310-1G>A Likely pathogenic ★★ same type
- FRAS1 c.3152-2A>G Likely pathogenic ★★ same type
- FRAS1 c.3563+1G>A Pathogenic ★★ same type
- FRAS1 c.7522+1G>T Pathogenic ★★ 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/fras1-p-ala1626val (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown