C7 c.138+12C>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +12 | near-intronic (+12 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.6 | GERP -1.5 |
| Non-coding constraint | Z -0.94 | 1 kb window · o/e 1.09 · regional · uncalibrated |
| Overall | ||
| CADD | 2.547 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,640 alleles
Filtering AF
0.000432%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000315%
Overall
0.000687%
11/1,602,328 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00134% | 74,640 |
| European (non-Finnish) | 0.000855% | 116,980 |
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
- Coding
- c.138+12C>A
- MANE Select
- NM_001565 · reported on NM_000587
- dbSNP
- rs767239431
- Type
- single nucleotide variant
- Location
- chr5:40931151 (GRCh38)
- Structure
- AlphaFold pLDDT 89.67 · 6 PDB
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-c-138-plus-12c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown