SRGAP1 p.Asn786=
c.2358C>T · rs12303060 · VCV785416
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 8.53%, afr) — too common for a highly-penetrant pathogenic allele
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 · C>G here scores Δ0.22 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -5.6 |
| Overall | ||
| CADD | 2.928 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.53%
African / African-American · 6,398/75,022 alleles
Filtering AF
8.35%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.28%
Overall
0.483%
7,792/1,614,080 alleles · common
exomes 4,018/1,461,826 · genomes 3,774/152,254 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 8.53% | 12 |
| Ashkenazi Jewishnot grpmax-eligible | 0.953% | 105 |
| Admixed American | 0.655% | 153 |
| Remaining individualsnot grpmax-eligible | 0.606% | 165 |
| Middle Eastern | 0.445% | 225 |
| South Asian | 0.0264% | 3,795 |
| European (non-Finnish) | 0.0241% | 4,155 |
| Finnishnot grpmax-eligible | 0.00469% | 21,341 |
| East Asian | 0.00446% | 22,434 |
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
- SRGAP1
- Protein
- p.Asn786=
- Coding
- c.2358C>T
- MANE Select
- NM_020762
- dbSNP
- rs12303060
- Type
- single nucleotide variant
- Location
- chr12:64126110 (GRCh38)
- Gene constraint
- LOEUF 0.47 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.49
- Residue 786
- the sh3 domain
Similar variants
- SRGAP1 p.Arg900Gly Uncertain significance ★★ ⚠ same type
- SRGAP1 c.2225-7G>A Likely benign ★★ same type
- SRGAP1 p.His875Arg Benign ★★ same type
- SRGAP1 p.His924= Benign ★★ same type
- SRGAP1 p.Ile371= Benign ★★ same type
- SRGAP1 p.Leu49= Benign/Likely benign ★★ same type
- SRGAP1 p.Leu953Val Benign ★★ same type
- SRGAP1 p.Ser569Gly 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/srgap1-p-asn786 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown