BARD1 c.2001+6T>C
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00879%, sas)
Conditions
2
hereditary neoplastic syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +6 | donor splice region (+6, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Pangolin | Δ0.28 | loss · gain 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 6 | GERP 2, phastCons 1 |
| Non-coding constraint | Z 0.88 | 1 kb window · o/e 0.92 · regional · uncalibrated |
| Overall | ||
| CADD | 19.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00879%
South Asian · 8/91,022 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00312%
Overall
0.000548%
8/1,458,956 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
- Coding
- c.2001+6T>C
- MANE Select
- NM_000465
- dbSNP
- rs775009517
- Type
- single nucleotide variant
- Location
- chr2:214730405 (GRCh38)
- Gene constraint
- LOEUF 1.087 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 64.82 · 11 PDB
Similar variants
- 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
- BARD1 c.1396-2A>C Likely pathogenic ★★ same condition
- BARD1 c.1568+1G>A Likely pathogenic ★★ same condition
- BARD1 c.1568+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-c-2001-plus-6t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown