CHRFAM7A p.Pro128=
c.384T>C · rs200611153 · VCV730496
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00407%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>T here scores Δ0.22 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -12 | |
| Overall | ||
| CADD | 0.671 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00407%
Admixed American · 2/49,146 alleles
Filtering AF
0.000687%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000543%
Overall
0.00118%
15/1,274,872 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00407% | 24,573 |
| African / African-American | 0.00213% | 46,894 |
| European (non-Finnish) | 0.00129% | 77,588 |
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
- CHRFAM7A
- Protein
- p.Pro128=
- Coding
- c.384T>C
- MANE Select
- NM_139320
- dbSNP
- rs200611153
- Type
- single nucleotide variant
- Location
- chr15:30372286 (GRCh38)
- Gene constraint
- LOEUF 0.697 · pLI 0.76 (gnomAD)
- Structure
- AlphaFold pLDDT 69.27
Similar variants
- CHRFAM7A p.Ala158Val Uncertain significance ★ ⚠ same type
- CHRFAM7A p.Ala208Thr Uncertain significance ★ ⚠ same type
- CHRFAM7A p.Arg115Thr Uncertain significance ★ ⚠ same type
- CHRFAM7A p.Arg264Cys Uncertain significance ★ ⚠ same type
- CHRFAM7A p.Arg273Cys Uncertain significance ★ ⚠ same type
- CHRFAM7A p.Asn103Ser Uncertain significance ★ ⚠ same type
- CHRFAM7A p.Asn291Asp Uncertain significance ★ ⚠ same type
- CHRFAM7A p.Asp167Gly 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/chrfam7a-p-pro128 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown