SEMA3A p.Ser67=
c.201T>C · rs144566280 · VCV725452
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0633%, 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 2.7 | GERP 0.003, phastCons 1 |
| Overall | ||
| CADD | 10.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0633%
European (non-Finnish) · 747/1,179,840 alleles
Filtering AF
0.0595%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.058%
Overall
0.0498%
804/1,613,666 alleles · ultra-rare
exomes 739/1,461,596 · genomes 65/152,070 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0633% | 1,579 |
| Remaining individualsnot grpmax-eligible | 0.0464% | 2,154 |
| Admixed American | 0.0233% | 4,283 |
| Finnishnot grpmax-eligible | 0.0109% | 9,145 |
| African / African-American | 0.00935% | 10,697 |
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.Ser67=
- Coding
- c.201T>C
- MANE Select
- NM_006080
- dbSNP
- rs144566280
- Type
- single nucleotide variant
- Location
- chr7:84134863 (GRCh38)
- Gene constraint
- LOEUF 0.453 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 84.50
- Residue 67
- 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-ser67 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown