CARMIL2 p.Ala294=
c.882A>T · rs200137927 · VCV1164530
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.681%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.25 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.20 | gain · loss 0.06 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -4.2 | GERP -3.1 |
| Overall | ||
| CADD | 0.614 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.681%
African / African-American · 508/74,542 alleles
Filtering AF
0.632%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.613%
Overall
0.0354%
566/1,599,636 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.681% | 147 |
| Admixed American | 0.0517% | 1,935 |
| Remaining individualsnot grpmax-eligible | 0.0355% | 2,818 |
| Middle Eastern | 0.0334% | 2,996 |
| South Asian | 0.00113% | 88,238 |
| European (non-Finnish) | 0.000255% | 391,443 |
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
- CARMIL2
- Protein
- p.Ala294=
- Coding
- c.882A>T
- MANE Select
- NM_001013838
- dbSNP
- rs200137927
- Type
- single nucleotide variant
- Location
- chr16:67647690 (GRCh38)
- Gene constraint
- LOEUF 0.701 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.50
Similar variants
- CARMIL2 c.1334+1G>T Likely pathogenic ★★ same type
- CARMIL2 c.2313+1G>A Likely pathogenic ★★ same type
- CARMIL2 c.871+1G>T Pathogenic ★★ same type
- CARMIL2 c.958+1G>A Likely pathogenic ★★ same type
- CARMIL2 p.Arg174Ter Pathogenic/Likely pathogenic ★★ same type
- CARMIL2 p.Asn530Lys Pathogenic/Likely pathogenic ★★ same type
- CARMIL2 p.Gln1379Ter Pathogenic/Likely pathogenic ★★ same type
- CARMIL2 p.Ser370Ter 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/carmil2-p-ala294 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown