SP7 p.Ala2=
c.6G>A · rs375712065 · VCV724912
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.282%, eas)
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 0.068 | GERP 0.58, phastCons 0.91 |
| Overall | ||
| CADD | 13.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.282%
East Asian · 116/41,124 alleles
Filtering AF
0.24%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.225%
Overall
0.0449%
693/1,544,072 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.282% | 355 |
| Admixed American | 0.13% | 771 |
| Remaining individualsnot grpmax-eligible | 0.125% | 800 |
| African / African-American | 0.0399% | 2,508 |
| European (non-Finnish) | 0.0353% | 2,835 |
| South Asian | 0.00595% | 16,804 |
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
- SP7
- Protein
- p.Ala2=
- Coding
- c.6G>A
- MANE Select
- NM_001173467
- dbSNP
- rs375712065
- Type
- single nucleotide variant
- Location
- chr12:53335641 (GRCh38)
- Gene constraint
- LOEUF 0.808 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 52.78
Similar variants
- SP7 p.Ala2Val Uncertain significance ★★ ⚠ same residue
- SP7 p.Arg267Cys Uncertain significance ★★ ⚠ same type
- SP7 p.Arg280Leu Uncertain significance ★★ ⚠ same type
- SP7 p.Arg280Trp Uncertain significance ★★ ⚠ same type
- SP7 p.Arg316His Uncertain significance ★★ ⚠ same type
- SP7 p.Arg350Trp Uncertain significance ★★ ⚠ same type
- SP7 p.Arg362His Uncertain significance ★★ ⚠ same type
- SP7 p.Arg365Ter 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/sp7-p-ala2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown