ASCC3 p.Arg160=
c.480G>A · VCV3905165
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0125%, 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 | GERP 0.15, phastCons 0.031 |
| Overall | ||
| CADD | 2.401 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0125%
European (non-Finnish) · 147/1,179,054 alleles
Filtering AF
0.0108%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0102%
Overall
0.00961%
155/1,612,100 alleles · ultra-rare
exomes 145/1,460,028 · genomes 10/152,072 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0125% | 8,021 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,599 |
| Admixed American | 0.00335% | 29,888 |
| African / African-American | 0.00268% | 37,379 |
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
- ASCC3
- Protein
- p.Arg160=
- Coding
- c.480G>A
- MANE Select
- NM_006828
- Type
- single nucleotide variant
- Location
- chr6:100848469 (GRCh38)
- Gene constraint
- LOEUF 0.677 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.93 · 2 PDB
- Residue 160
- the 'required for interaction with ascc2' region
Similar variants
- ASCC3 c.1597-2A>G Likely pathogenic ★★ same type
- ASCC3 c.1596+1G>T Uncertain significance ★★ same type
- ASCC3 p.Ala1186Val Uncertain significance ★★ ⚠ same type
- ASCC3 p.Ala94Val Uncertain significance ★★ ⚠ same type
- ASCC3 p.Arg1808His Uncertain significance ★★ ⚠ same type
- ASCC3 p.Arg1835Cys Uncertain significance ★★ ⚠ same type
- ASCC3 p.Arg630Cys Uncertain significance ★★ ⚠ same type
- ASCC3 p.Asn1607Ser Uncertain significance ★★ ⚠ 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/ascc3-p-arg160 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown