ASCC1 p.Arg256=
c.766C>A · VCV3624289
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00509%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>A here scores Δ0.21 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.3 | GERP 0.059, phastCons 1 |
| Overall | ||
| CADD | 8.24 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00509%
European (non-Finnish) · 60/1,179,854 alleles
Filtering AF
0.00402%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00362%
Overall
0.00384%
62/1,613,788 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00509% | 19,664 |
| African / African-American | 0.00267% | 37,452 |
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
- ASCC1
- Protein
- p.Arg256=
- Coding
- c.766C>A
- MANE Select
- NM_001198800
- Type
- single nucleotide variant
- Location
- chr10:72133162 (GRCh38)
- Gene constraint
- LOEUF 1.002 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.70 · 1 PDB
- Residue 256
- a β-strand
Similar variants
- ASCC1 p.Arg256Ter Likely pathogenic ★ same residue
- ASCC1 c.311-2A>G Pathogenic ★★ same type
- ASCC1 c.626+1G>A Pathogenic/Likely pathogenic ★★ same type
- ASCC1 c.871+1G>A Pathogenic/Likely pathogenic ★★ same type
- ASCC1 p.Arg110Ter Pathogenic ★★ same type
- ASCC1 p.Arg117Ter Pathogenic ★★ same type
- ASCC1 p.Arg128Ter Pathogenic ★★ same type
- ASCC1 p.Gln195Ter 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/ascc1-p-arg256 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown