ARID1B p.Tyr1663=
c.4989C>T · rs2068129 · VCV1257085
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.12%, 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 4 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 9.987 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.12%
African / African-American · 90/75,042 alleles
Filtering AF
0.0999%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0924%
Overall
0.00632%
102/1,613,908 alleles · rare
exomes 46/1,461,602 · genomes 56/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.12% | 834 |
| Admixed American | 0.0133% | 7,503 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,247 |
| European (non-Finnish) | 0.00017% | 589,936 |
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
- ARID1B
- Protein
- p.Tyr1663=
- Coding
- c.4989C>T
- MANE Select
- NM_001374828
- dbSNP
- rs2068129
- Type
- single nucleotide variant
- Location
- chr6:157201214 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 47.16 · 9 PDB
Similar variants
- ARID1B c.1987-29738G>T Pathogenic ★★ same type
- ARID1B c.2248-2A>G Pathogenic/Likely pathogenic ★★ same type
- ARID1B c.2762-1G>C Likely pathogenic ★★ same type
- ARID1B c.3505-2A>G Pathogenic ★★ same type
- ARID1B c.4058+1G>C Pathogenic ★★ same type
- ARID1B c.4383-1G>A Pathogenic ★★ same type
- ARID1B c.4479+1G>T Pathogenic ★★ same type
- ARID1B c.5264-2A>G Pathogenic/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/arid1b-p-tyr1663 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown