BARD1 p.Pro464=
c.1392A>G · rs2106081063 · VCV1081579
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 6.86e-05%)
Conditions
2
hereditary neoplastic syndrome
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 -0.19 | GERP -0.64, phastCons 0.001 |
| Overall | ||
| CADD | 10.24 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.86e-05%
Overall
6.86e-05%
1/1,457,816 alleles · very 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
- BARD1
- Protein
- p.Pro464=
- Coding
- c.1392A>G
- MANE Select
- NM_000465
- dbSNP
- rs2106081063
- Type
- single nucleotide variant
- Location
- chr2:214769235 (GRCh38)
- Gene constraint
- LOEUF 1.087 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 64.82 · 11 PDB
- Residue 464
- an α-helix
Similar variants
- BARD1 p.Pro464Arg Uncertain significance ★★ ⚠ same residue
- BARD1 p.Pro464Leu Uncertain significance ★★ ⚠ same residue
- BARD1 p.Pro464Ser Uncertain significance ★★ ⚠ same residue
- BARD1 c.1314+1G>A Pathogenic/Likely pathogenic ★★ same condition
- BARD1 c.1314+1G>T Likely pathogenic ★★ same condition
- BARD1 c.1396-1G>A Likely pathogenic ★★ same condition
- BARD1 c.1396-1G>C Likely pathogenic ★★ same condition
- BARD1 c.1396-1G>T Likely pathogenic ★★ 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/bard1-p-pro464 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown