Is CFAP47 p.Lys628= (c.1884A>G) pathogenic?

CFAP47 p.Lys628= (c.1884A>G) is classified Likely benign in CFAP47 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-01). Very rare (popmax 0.00057%, nfe).

How common is CFAP47 p.Lys628= (c.1884A>G) in the general population?

CFAP47 p.Lys628= (c.1884A>G) is very rare (popmax 0.00057%, nfe) (gnomAD).

CFAP47 p.Lys628=

c.1884A>G · rs2518940751 · VCV2660261

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00057%, 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 2.8	GERP 0.051, phastCons 0.32
Overall
CADD	0.949	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00057% European (non-Finnish) · 5/877,734 alleles

Filtering AF 0.000167% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000121%

Overall 0.000421% 5/1,186,337 alleles · very rare exomes 5/1,072,547 · genomes 0/113,790 · joint denominator

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.Lys628=
Coding: c.1884A>G
MANE Select: NM_001304548
dbSNP: rs2518940751
Type: single nucleotide variant
Location: chrX:35970837 (GRCh38)

Full CFAP47 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-lys628 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown