CFAP47 p.Val1648=
c.4944C>A · rs146431612 · VCV2660265
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0354%, afr)
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 0.85 | GERP -3.2, phastCons 0.013 |
| Overall | ||
| CADD | 0.206 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0354%
African / African-American · 20/56,472 alleles
Filtering AF
0.0234%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0196%
Overall
0.00329%
39/1,185,521 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0354% | 2,824 |
| South Asian | 0.0296% | 3,380 |
| Remaining individualsnot grpmax-eligible | 0.00644% | 15,524 |
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
- CFAP47
- Protein
- p.Val1648=
- Coding
- c.4944C>A
- MANE Select
- NM_001304548
- dbSNP
- rs146431612
- Type
- single nucleotide variant
- Location
- chrX:36098820 (GRCh38)
Similar variants
- CFAP47 p.Ser964Gly Uncertain significance ★★ same type
- CFAP47 p.Thr2847Met Likely benign ★★ same type
- CFAP47 c.3652-4G>C Uncertain significance ★ same type
- CFAP47 p.Ala566Ser Uncertain significance ★ ⚠ same type
- CFAP47 p.Arg429Cys Uncertain significance ★ ⚠ same type
- CFAP47 p.Asp1565Val Uncertain significance ★ same type
- CFAP47 p.Gln2891His Uncertain significance ★ same type
- CFAP47 p.Gln439Pro 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/cfap47-p-val1648 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown