ARID1A p.Pro208=
c.624C>A · rs770301214 · VCV1607017
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000262%, nfe)
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 2.3 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 12.99 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000262%
European (non-Finnish) · 3/1,146,428 alleles
Filtering AF
7e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000216%
3/1,386,490 alleles · very rare
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
- ARID1A
- Protein
- p.Pro208=
- Coding
- c.624C>A
- MANE Select
- NM_006015
- dbSNP
- rs770301214
- Type
- single nucleotide variant
- Location
- chr1:26697027 (GRCh38)
- Gene constraint
- LOEUF 0.141 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 47.81 · 7 PDB
- Residue 208
- the 'disordered' region
Similar variants
- ARID1A p.Pro208Ser Benign ★ same residue
- ARID1A p.Pro208Thr Benign ★ same residue
- ARID1A c.1920+5G>A Likely pathogenic ★★ same type
- ARID1A c.3198+5G>A Likely pathogenic ★★ same type
- ARID1A p.Ala1077Glu Pathogenic/Likely pathogenic ★★ same type
- ARID1A p.Arg1020Lys Likely pathogenic ★★ same type
- ARID1A p.Gln1367= Likely pathogenic ★★ same type
- ARID1A p.Gln199Ter Likely 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/arid1a-p-pro208 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown