SP7 p.Ser55=
c.165A>G · rs371022356 · VCV2416390
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00483%, 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 -4.6 | GERP -3.5 |
| Overall | ||
| CADD | 1.301 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00483%
European (non-Finnish) · 57/1,179,892 alleles
Filtering AF
0.00378%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00345%
Overall
0.00353%
57/1,613,730 alleles · very rare
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.Ser55=
- Coding
- c.165A>G
- MANE Select
- NM_001173467
- dbSNP
- rs371022356
- Type
- single nucleotide variant
- Location
- chr12:53329277 (GRCh38)
- Gene constraint
- LOEUF 0.808 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 52.78
- Residue 55
- the 'disordered' region
Similar variants
- SP7 p.Ala2Val Uncertain significance ★★ ⚠ same type
- 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-ser55 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown