DSCAM p.Asn1250=
c.3750C>T · rs41445251 · VCV770009
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.72%, amr)
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 7.4 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 9.455 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.72%
Admixed American · 1,632/59,994 alleles
Filtering AF
2.61%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.57%
Overall
0.186%
3,003/1,613,946 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 2.72% | 37 |
| East Asian | 2.11% | 47 |
| Remaining individualsnot grpmax-eligible | 0.331% | 302 |
| African / African-American | 0.125% | 798 |
| South Asian | 0.0472% | 2,118 |
| Finnishnot grpmax-eligible | 0.0313% | 3,198 |
| European (non-Finnish) | 0.00517% | 19,344 |
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.Asn1250=
- Coding
- c.3750C>T
- MANE Select
- NM_001389
- dbSNP
- rs41445251
- Type
- single nucleotide variant
- Location
- chr21:40093821 (GRCh38)
- Gene constraint
- LOEUF 0.28 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.98 · 1 PDB
- Residue 1250
- the fibronectin type-iii 4 domain
Similar variants
- DSCAM p.Ser682Arg Uncertain significance ★★ ⚠ same type
- DSCAM c.5383+9T>A Benign ★★ same type
- DSCAM p.Ala153= Benign ★★ same type
- DSCAM p.Arg1798= Benign/Likely 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-asn1250 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown