REV3L p.Pro2172=
c.6516C>G · rs1414564926 · VCV709413
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP -1.7, phastCons 1 |
| Overall | ||
| CADD | 6.42 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
African / African-American · 5/74,816 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00162%
Overall
0.000806%
13/1,613,144 alleles · very rare
exomes 9/1,460,976 · genomes 4/152,168 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00668% | 14,963 |
| European (non-Finnish) | 0.000678% | 147,478 |
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
- REV3L
- Protein
- p.Pro2172=
- Coding
- c.6516C>G
- MANE Select
- NM_001372078
- dbSNP
- rs1414564926
- Type
- single nucleotide variant
- Location
- chr6:111367272 (GRCh38)
- Gene constraint
- LOEUF 0.261 · pLI 1.00 (gnomAD)
Similar variants
- REV3L p.Arg1970Cys Uncertain significance ★★ ⚠ same type
- REV3L p.Ala565= Benign ★★ same type
- REV3L p.Glu2015Val Benign/Likely benign ★★ same type
- REV3L p.Gly1721= Benign/Likely benign ★★ same type
- REV3L p.His367= Likely benign ★★ same type
- REV3L p.Ile1327Val Benign/Likely benign ★★ same type
- REV3L p.Leu2213= Likely benign ★★ same type
- REV3L p.Lys1158Asn Benign/Likely benign ★★ 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/rev3l-p-pro2172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown