Is BARD1 p.Asp3Tyr (c.7G>T) pathogenic?

BARD1 p.Asp3Tyr (c.7G>T) is classified Uncertain significance in BARD1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2021-12-23). AlphaMissense: likely benign (0.1287); Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with BARD1 p.Asp3Tyr (c.7G>T)?

BARD1 p.Asp3Tyr (c.7G>T) is associated with hereditary neoplastic syndrome, hereditary breast carcinoma (ClinVar).

How common is BARD1 p.Asp3Tyr (c.7G>T) in the general population?

BARD1 p.Asp3Tyr (c.7G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BARD1 p.Asp3Tyr (c.7G>T)?

AlphaMissense predicts likely benign (score 0.1287) — an in-silico prediction, not a clinical call.

BARD1 p.Asp3Tyr

c.7G>T · rs1060501282 · VCV584634

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1287 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.1287	likely benign
REVEL	0.134	moderately benign-leaning
SaProt	LLR -7.43	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.86	GERP 1.1
Regional constraint	o/e 1.06	unconstrained · MANE · 81 kb · p 0.077 · regional, not allelic
Overall
CADD	15.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BARD1
Protein: p.Asp3Tyr
Coding: c.7G>T
MANE Select: NM_000465
dbSNP: rs1060501282
Type: single nucleotide variant
Location: chr2:214809563 (GRCh38)
Gene constraint: LOEUF 1.087 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 64.82 · 11 PDB
Residue 3: the 'disordered' region

Full BARD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary breast carcinoma

Similar variants

BARD1 p.Asp3Asn Uncertain significance ★★ ⚠ same residue
BARD1 p.Asp3Ala Uncertain significance ★ ⚠ same residue
BARD1 p.Asp3Glu Uncertain significance ★ ⚠ same residue
BARD1 p.Asp3Gly Uncertain significance ★ ⚠ same residue
BARD1 p.Asp3His Uncertain significance ★ ⚠ same residue
BARD1 p.Asp3Val Uncertain significance ★ ⚠ same residue
BARD1 p.Asp3= Likely benign ★ same residue
BARD1 p.Asp3fs Pathogenic ★ same residue

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/bard1-p-asp3tyr (accessed [today's date]).

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