C7 p.Val54=
c.162G>A · rs371288921 · VCV2112664
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, 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 0.34 | GERP -4.8, phastCons 1 |
| Overall | ||
| CADD | 2.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,868 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000248%
4/1,612,832 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,868 |
| African / African-American | 0.00134% | 74,880 |
| European (non-Finnish) | 0.00017% | 589,689 |
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
- C7
- Protein
- p.Val54=
- Coding
- c.162G>A
- MANE Select
- NM_001565 · reported on NM_000587
- dbSNP
- rs371288921
- Type
- single nucleotide variant
- Location
- chr5:40934348 (GRCh38)
- Structure
- AlphaFold pLDDT 89.67 · 6 PDB
- Residue 54
- a disulfide bond
Similar variants
- C7 c.281-1G>T Pathogenic/Likely pathogenic ★★ same type
- C7 c.63-1G>A Pathogenic ★★ same type
- C7 c.739-2A>G Likely pathogenic ★★ same type
- C7 p.Arg402Ter Pathogenic/Likely pathogenic ★★ same type
- C7 p.Gln271Ter Pathogenic/Likely pathogenic ★★ same type
- C7 p.Gly379Arg Pathogenic/Likely pathogenic ★★ same type
- C7 p.Trp205Ter Pathogenic/Likely pathogenic ★★ same type
- C7 p.Ala359Thr 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/c7-p-val54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown