SEMA3A p.Phe80=
c.240C>T · rs775348886 · VCV732609
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.129%, 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 9.9 | GERP 2.7, phastCons 1 |
| Overall | ||
| CADD | 15.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.129%
Admixed American · 77/59,742 alleles
Filtering AF
0.106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0972%
Overall
0.00726%
117/1,612,476 alleles · rare
exomes 106/1,460,362 · genomes 11/152,114 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.129% | 776 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,673 |
| African / African-American | 0.00668% | 14,966 |
| East Asian | 0.00223% | 44,774 |
| European (non-Finnish) | 0.00195% | 51,275 |
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
- SEMA3A
- Protein
- p.Phe80=
- Coding
- c.240C>T
- MANE Select
- NM_006080
- dbSNP
- rs775348886
- Type
- single nucleotide variant
- Location
- chr7:84134824 (GRCh38)
- Gene constraint
- LOEUF 0.453 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 84.50
- Residue 80
- the sema domain
Similar variants
- SEMA3A p.Ala491Thr Uncertain significance ★★ ⚠ same type
- SEMA3A p.Ala523Val Uncertain significance ★★ ⚠ same type
- SEMA3A p.Arg419His Uncertain significance ★★ ⚠ same type
- SEMA3A p.Arg516Trp Uncertain significance ★★ ⚠ same type
- SEMA3A p.Arg617Ter Uncertain significance ★★ same type
- SEMA3A p.Arg637His Uncertain significance ★★ ⚠ same type
- SEMA3A p.Arg66Trp Uncertain significance ★★ ⚠ same type
- SEMA3A p.Arg733Cys 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/sema3a-p-phe80 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown