Is BICC1 p.Ala2= (c.6C>T) pathogenic?

BICC1 p.Ala2= (c.6C>T) is classified Likely benign in BICC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-23). Ultra-rare (popmax 0.0152%, amr).

How common is BICC1 p.Ala2= (c.6C>T) in the general population?

BICC1 p.Ala2= (c.6C>T) is ultra-rare (popmax 0.0152%, amr) (gnomAD).

BICC1 p.Ala2=

c.6C>T · VCV3717925

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0152%, amr)

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 1.5	GERP 0.87, phastCons 1
Overall
CADD	14.8	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0152% Admixed American · 7/45,914 alleles

Filtering AF 0.00711% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00505%

Overall 0.000461% 7/1,518,052 alleles · ultra-rare

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: BICC1
Protein: p.Ala2=
Coding: c.6C>T
MANE Select: NM_001080512
Type: single nucleotide variant
Location: chr10:58513149 (GRCh38)
Gene constraint: LOEUF 0.541 · pLI 0.30 (gnomAD)
Structure: AlphaFold pLDDT 61.02 · 3 PDB
Residue 2: the 'disordered' region

Full BICC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BICC1 p.Ala190Thr Uncertain significance ★★ ⚠ same type
BICC1 p.Ala276Ser Uncertain significance ★★ ⚠ same type
BICC1 p.Ala523Val Uncertain significance ★★ ⚠ same type
BICC1 p.Arg302Gln Uncertain significance ★★ ⚠ same type
BICC1 p.Arg657Lys Uncertain significance ★★ ⚠ same type
BICC1 p.Arg804His Uncertain significance ★★ ⚠ same type
BICC1 p.Arg839His Uncertain significance ★★ ⚠ same type
BICC1 p.Arg961Cys 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/bicc1-p-ala2 (accessed [today's date]).

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