SIN3B p.Ser253=
c.759C>T · rs773875029 · VCV3052153
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.147%, amr)
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 -11 | GERP -3.5 |
| Overall | ||
| CADD | 0.391 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.147%
Admixed American · 87/59,372 alleles
Filtering AF
0.122%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.112%
Overall
0.0101%
163/1,608,070 alleles · rare
exomes 158/1,455,822 · genomes 5/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.147% | 682 |
| South Asian | 0.0501% | 1,994 |
| Remaining individualsnot grpmax-eligible | 0.0225% | 4,451 |
| Middle Eastern | 0.0165% | 6,064 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00339% | 29,538 |
| European (non-Finnish) | 0.00127% | 78,502 |
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
- SIN3B
- Protein
- p.Ser253=
- Coding
- c.759C>T
- MANE Select
- NM_001297595
- dbSNP
- rs773875029
- Type
- single nucleotide variant
- Location
- chr19:16851444 (GRCh38)
- Gene constraint
- LOEUF 0.245 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.07 · 4 PDB
- Residue 253
- the 'interaction with cry1' region; the 'disordered' region
Similar variants
- SIN3B p.Ala534Thr Uncertain significance ★★ same type
- SIN3B p.Glu258Asp Uncertain significance ★★ ⚠ same type
- SIN3B p.His91Tyr Uncertain significance ★★ ⚠ same type
- SIN3B p.Pro281Ala Uncertain significance ★★ ⚠ same type
- SIN3B p.Val160Met Uncertain significance ★★ ⚠ same type
- SIN3B p.Val873Ile Uncertain significance ★★ ⚠ same type
- SIN3B c.1266+354G>A Benign ★★ same type
- SIN3B c.2954+6A>G 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/sin3b-p-ser253 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown