ROM1 p.Phe239=
c.717C>T · rs762983591 · VCV1161242
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.287 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -3.1 |
| Overall | ||
| CADD | 0.503 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.000496%
8/1,614,038 alleles · ultra-rare
exomes 7/1,461,878 · genomes 1/152,160 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| Admixed American | 0.005% | 20,002 |
| European (non-Finnish) | 0.000339% | 295,009 |
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.Phe239=
- Coding
- c.717C>T
- MANE Select
- NM_000327
- dbSNP
- rs762983591
- Type
- single nucleotide variant
- Location
- chr11:62614384 (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-phe239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown