Is BCLAF1 p.Val467= (c.1401A>G) pathogenic?

BCLAF1 p.Val467= (c.1401A>G) is classified Likely benign in BCLAF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-03). Common (popmax 7.01%, afr) — too common for a highly-penetrant pathogenic allele.

BCLAF1 p.Val467=

Q: How common is BCLAF1 p.Val467= (c.1401A>G) in the general population?

BCLAF1 p.Val467= (c.1401A>G) is common (popmax 7.01%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1401A>G · rs1967444 · VCV1771799

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 7.01%, afr) — too common for a highly-penetrant pathogenic allele

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 4.2	GERP 0.59, phastCons 1
Overall
CADD	8.595	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 7.01% African / African-American · 4,604/65,676 alleles

Filtering AF 6.84% ClinGen BA1/BS1 input FAF95, joint · FAF99 6.77%

Overall 0.435% 6,950/1,597,022 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	7.01%	14
Middle Eastern	2.34%	43
Amishnot grpmax-eligible	1.84%	54
Ashkenazi Jewishnot grpmax-eligible	1.35%	74
Remaining individualsnot grpmax-eligible	0.664%	151
Admixed American	0.496%	201
South Asian	0.275%	363
European (non-Finnish)	0.0731%	1,367
Finnishnot grpmax-eligible	0.00313%	31,979

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: BCLAF1
Protein: p.Val467=
Coding: c.1401A>G
MANE Select: NM_014739
dbSNP: rs1967444
Type: single nucleotide variant
Location: chr6:136276124 (GRCh38)
Gene constraint: LOEUF 0.213 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 47.04 · 2 PDB
Residue 467: the 'disordered' region

Full BCLAF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BCLAF1 p.Gly210Ser Benign/Likely benign ★★ same type
BCLAF1 c.2397+1G>C Uncertain significance ★ same type
BCLAF1 p.Ala169Thr Uncertain significance ★ ⚠ same type
BCLAF1 p.Ala310Val Uncertain significance ★ ⚠ same type
BCLAF1 p.Ala669Val Uncertain significance ★ ⚠ same type
BCLAF1 p.Arg107Gln Uncertain significance ★ ⚠ same type
BCLAF1 p.Arg111His Uncertain significance ★ ⚠ same type
BCLAF1 p.Arg126Lys 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/bclaf1-p-val467 (accessed [today's date]).

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