DSCAM p.Ala153=
c.459G>A · rs79669041 · VCV778181
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.25%, 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 -0.49 | GERP -3.4, phastCons 0.051 |
| Overall | ||
| CADD | 13.98 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.25%
European (non-Finnish) · 14,716/1,179,880 alleles
Filtering AF
1.23%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.22%
Overall
1.03%
16,630/1,613,904 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.25% | 80 |
| Finnishnot grpmax-eligible | 0.959% | 104 |
| Remaining individualsnot grpmax-eligible | 0.802% | 125 |
| Admixed American | 0.548% | 182 |
| Ashkenazi Jewishnot grpmax-eligible | 0.48% | 208 |
| Amishnot grpmax-eligible | 0.439% | 228 |
| South Asian | 0.2% | 500 |
| African / African-American | 0.188% | 532 |
| Middle Eastern | 0.0165% | 6,060 |
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
- DSCAM
- Protein
- p.Ala153=
- Coding
- c.459G>A
- MANE Select
- NM_001389
- dbSNP
- rs79669041
- Type
- single nucleotide variant
- Location
- chr21:40692859 (GRCh38)
- Gene constraint
- LOEUF 0.28 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.98 · 1 PDB
- Residue 153
- a disulfide bond; the ig-like c2-type 2 domain
Similar variants
- DSCAM p.Ser682Arg Uncertain significance ★★ ⚠ same type
- DSCAM c.5383+9T>A Benign ★★ same type
- DSCAM p.Arg1798= Benign/Likely benign ★★ same type
- DSCAM p.Asn1250= Benign ★★ same type
- DSCAM p.Asn576= Benign/Likely benign ★★ same type
- DSCAM p.Asp185= Benign/Likely benign ★★ same type
- DSCAM p.Gln582= Benign ★★ same type
- DSCAM p.Gly1502= Likely 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/dscam-p-ala153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown