Is BFSP1 c.735+17C>T pathogenic?

BFSP1 c.735+17C>T is classified Likely benign in BFSP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-23). Ultra-rare (popmax 0.0179%, mid); Associated with cataract 33.

What condition is associated with BFSP1 c.735+17C>T?

BFSP1 c.735+17C>T is associated with cataract 33 (ClinVar).

How common is BFSP1 c.735+17C>T in the general population?

BFSP1 c.735+17C>T is ultra-rare (popmax 0.0179%, mid) (gnomAD).

BFSP1 c.735+17C>T

rs368674829 · VCV1635959

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0179%, mid)

Conditions

cataract 33

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +17	near-intronic (+17 nt from the splice site)
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.45	GERP -1.6
Overall
CADD	1.167	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0179% Middle Eastern · 1/5,596 alleles

Filtering AF 0.004% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00282%

Overall 0.00329% 51/1,550,528 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0179%	5,596
Remaining individualsnot grpmax-eligible	0.015%	6,654
East Asian	0.0095%	10,522
South Asian	0.00869%	11,501
Admixed American	0.00797%	12,542
European (non-Finnish)	0.00209%	47,928
Finnishnot grpmax-eligible	0.00163%	61,464
African / African-American	0.00137%	72,934

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: BFSP1
Coding: c.735+17C>T
MANE Select: NM_001195
dbSNP: rs368674829
Type: single nucleotide variant
Location: chr20:17508872 (GRCh38)
Gene constraint: LOEUF 1.371 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.66

Full BFSP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

cataract 33 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BFSP1 p.Ala643Thr Uncertain significance ★★ ⚠ same condition
BFSP1 p.Arg560Cys Uncertain significance ★★ ⚠ same condition
BFSP1 p.Arg69Trp Uncertain significance ★★ ⚠ same condition
BFSP1 p.Asp19Asn Uncertain significance ★★ ⚠ same condition
BFSP1 p.Gln294Arg Uncertain significance ★★ ⚠ same condition
BFSP1 p.Gly46Trp Uncertain significance ★★ ⚠ same condition
BFSP1 p.Ile271Thr Uncertain significance ★★ ⚠ same condition
BFSP1 p.Leu68Phe Uncertain significance ★★ ⚠ same condition

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/bfsp1-c-735-plus-17c-t (accessed [today's date]).

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