ROM1 p.Ala29=
c.87G>A · rs531154214 · VCV1929541
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00334%, amr)
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 0.14 | GERP -2.6 |
| Overall | ||
| CADD | 4.554 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00334%
Admixed American · 2/59,950 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000682%
11/1,613,574 alleles · very rare
exomes 7/1,461,220 · genomes 4/152,354 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00334% | 29,975 |
| African / African-American | 0.00266% | 37,530 |
| South Asian | 0.0022% | 45,491 |
| European (non-Finnish) | 0.000424% | 235,963 |
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
- ROM1
- Protein
- p.Ala29=
- Coding
- c.87G>A
- MANE Select
- NM_000327
- dbSNP
- rs531154214
- Type
- single nucleotide variant
- Location
- chr11:62613368 (GRCh38)
- Gene constraint
- LOEUF 1.003 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.56 · 1 PDB
Similar variants
- ROM1 p.Ala132Val Uncertain significance ★★ ⚠ same type
- ROM1 p.Ala140Thr Uncertain significance ★★ ⚠ same type
- ROM1 p.Ala265Thr Uncertain significance ★★ ⚠ same type
- ROM1 p.Ala329Val Uncertain significance ★★ ⚠ same type
- ROM1 p.Ala54Thr Uncertain significance ★★ ⚠ same type
- ROM1 p.Ala69Gly Uncertain significance ★★ ⚠ same type
- ROM1 p.Ala71Thr Uncertain significance ★★ ⚠ same type
- ROM1 p.Ala71Val 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/rom1-p-ala29 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown