BRIP1 c.2575+10C>T
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 8.52e-05%, nfe)
Conditions
3
Fanconi anemia complementation group J
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +10 | near-intronic (+10 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.25 | GERP -0.7, phastCons 0.056 |
| Non-coding constraint | Z 4.23 | 1 kb window · o/e 0.71 · regional · uncalibrated |
| Overall | ||
| CADD | 8.988 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.52e-05%
European (non-Finnish) · 1/1,173,344 alleles
Overall
6.88e-05%
1/1,454,482 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
- BRIP1
- Coding
- c.2575+10C>T
- MANE Select
- NM_032043
- dbSNP
- rs1060504322
- Type
- single nucleotide variant
- Location
- chr17:61693420 (GRCh38)
- Gene constraint
- LOEUF 0.848 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 64.19 · 6 PDB
Similar variants
- BRIP1 c.1140+1G>A Likely pathogenic ★★ same condition
- BRIP1 c.1141-2A>C Likely pathogenic ★★ same condition
- BRIP1 c.1141-2A>G Likely pathogenic ★★ same condition
- BRIP1 c.1141-2A>T Likely pathogenic ★★ same condition
- BRIP1 c.1340+1G>A Pathogenic/Likely pathogenic ★★ same condition
- BRIP1 c.1341-1G>A Likely pathogenic ★★ same condition
- BRIP1 c.1341-1G>C Likely pathogenic ★★ same condition
- BRIP1 c.1341-2A>C 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/brip1-c-2575-plus-10c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown