ASCC1 p.Asp100=
c.300C>T · rs752290786 · VCV1545858
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.011%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.025 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.21 | GERP -3.4, phastCons 0.21 |
| Overall | ||
| CADD | 0.411 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.011%
South Asian · 10/91,046 alleles
Filtering AF
0.00594%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00453%
Overall
0.00186%
30/1,611,860 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.011% | 9,105 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,586 |
| Admixed American | 0.00167% | 59,984 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,426 |
| European (non-Finnish) | 0.00136% | 73,639 |
| African / African-American | 0.00134% | 74,840 |
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.Asp100=
- Coding
- c.300C>T
- MANE Select
- NM_001198800
- dbSNP
- rs752290786
- Type
- single nucleotide variant
- Location
- chr10:72203437 (GRCh38)
- Gene constraint
- LOEUF 1.002 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.70 · 1 PDB
- Residue 100
- the kh domain
Similar variants
- ASCC1 p.Asp100Glu Uncertain significance ★ ⚠ 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-asp100 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown