ROM1 p.Ala71=
c.213G>A · rs886042979 · VCV284916
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -4.8 | GERP -3.1 |
| Overall | ||
| CADD | 2.473 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,054 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000434%
7/1,613,740 alleles · ultra-rare
exomes 7/1,461,418 · genomes 0/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,054 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,590 |
| East Asian | 0.00223% | 44,864 |
| South Asian | 0.0022% | 45,529 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,468 |
| European (non-Finnish) | 8.48e-05% | 1,179,823 |
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.Ala71=
- Coding
- c.213G>A
- MANE Select
- NM_000327
- dbSNP
- rs886042979
- Type
- single nucleotide variant
- Location
- chr11:62613494 (GRCh38)
- Gene constraint
- LOEUF 1.003 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.56 · 1 PDB
Similar variants
- ROM1 p.Ala71Thr Uncertain significance ★★ ⚠ same residue
- ROM1 p.Ala71Val Uncertain significance ★★ ⚠ same residue
- 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
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-ala71 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown