AVPR2 c.910+13G>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00438%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.059 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| Splice region | donor +13 | near-intronic (+13 nt from the splice site) |
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.62 | GERP -3.1 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 0.176 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00438%
European (non-Finnish) · 39/890,985 alleles
Filtering AF
0.00328%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00288%
Overall
0.00349%
42/1,203,902 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00438% | 22,846 |
| Remaining individualsnot grpmax-eligible | 0.00423% | 23,646 |
| African / African-American | 0.00174% | 57,375 |
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
- AVPR2
- Coding
- c.910+13G>A
- MANE Select
- NM_000054
- dbSNP
- rs980699555
- Type
- single nucleotide variant
- Location
- chrX:153906429 (GRCh38)
- Structure
- AlphaFold pLDDT 76.84 · 44 PDB
Similar variants
- AVPR2 p.Arg104Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- AVPR2 p.Arg113Trp Pathogenic ★★ same type
- AVPR2 p.Arg137Cys Pathogenic ★★ same type
- AVPR2 p.Arg137His Pathogenic ★★ same type
- AVPR2 p.Arg181Cys Pathogenic ★★ ⚠ same type
- AVPR2 p.Arg202Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- AVPR2 p.Arg337Ter Pathogenic ★★ same type
- AVPR2 p.Asp85Asn 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/avpr2-c-910-plus-13g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown