Is CFAP47 c.5127+7T>C pathogenic?

CFAP47 c.5127+7T>C is classified Likely benign in CFAP47 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-01). Ultra-rare (popmax 0.0548%, mid).

How common is CFAP47 c.5127+7T>C in the general population?

CFAP47 c.5127+7T>C is ultra-rare (popmax 0.0548%, mid) (gnomAD).

CFAP47 c.5127+7T>C

rs375490296 · VCV2660266

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0548%, mid)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +7	near-intronic (+7 nt from the splice site) · inside the BP7-excluded zone
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.95	GERP -3.5
Non-coding constraint	—	not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained
Overall
CADD	0.401	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0548% Middle Eastern · 2/3,651 alleles

Filtering AF 0.0194% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0183%

Overall 0.0271% 249/919,172 alleles · ultra-rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.2%	499
Middle Easterngrpmax	0.0548%	1,826
European (non-Finnish)	0.0225%	4,451
Remaining individualsnot grpmax-eligible	0.0187%	5,350
Ashkenazi Jewishnot grpmax-eligible	0.0104%	9,653
South Asian	0.00646%	15,488

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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
Coding: c.5127+7T>C
MANE Select: NM_001304548
dbSNP: rs375490296
Type: single nucleotide variant
Location: chrX:36099886 (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-c-5127-plus-7t-c (accessed [today's date]).

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