The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • cspecId property did not resolve into a valid CSPEC request: https://cspec.genome.network/cspec-priv/SequenceVariantInterpretation/id/1530970171!
  • cspec.ruleSetIri property did not resolve into a valid CSPEC request: https://cspec.genome.network/cspec-priv/RuleSet/id/1530970184!
  • No CSPEC computed assertion could be determined for this classification!

  • No Criteria Specification was provided in the publication event for the variant classifaction.
  • The Criteria Specification shown below is a best-estimate based on the VCEP, gene, disease, and publication date.

Variant: NM_007294.4(BRCA1):c.132C>T (p.Cys44=)

CA10580710

230061 (ClinVar)

Gene: BRCA1 (HGNC:672)
Condition: BRCA1-related cancer predisposition (MONDO:0700268)
Inheritance Mode: Autosomal dominant inheritance
UUID: f4b09e6f-931d-4187-98a3-106e39e2f87c
Approved on: 2026-08-28
Published on: 2026-08-27

HGVS expressions

NM_007294.4:c.132C>T
NM_007294.4(BRCA1):c.132C>T (p.Cys44=)
NC_000017.11:g.43115728G>A
CM000679.2:g.43115728G>A
NC_000017.10:g.41267745G>A
CM000679.1:g.41267745G>A
NC_000017.9:g.38521271G>A
NG_005905.2:g.102256C>T
ENST00000354071.8:n.196C>T
ENST00000461574.2:c.132C>T
ENST00000470026.6:c.132C>T
ENST00000473961.6:c.132C>T
ENST00000476777.6:c.132C>T
ENST00000477152.6:c.132C>T
ENST00000478531.6:c.132C>T
ENST00000489037.2:c.132C>T
ENST00000493919.6:c.-8+8289C>T
ENST00000494123.6:c.132C>T
ENST00000497488.2:c.-219+9543C>T
ENST00000618469.2:c.132C>T
ENST00000634433.2:c.132C>T
ENST00000644379.2:c.132C>T
ENST00000644555.2:c.-10C>T
ENST00000652672.2:c.-10C>T
ENST00000484087.6:c.132C>T
ENST00000700182.1:c.132C>T
ENST00000700183.1:c.132C>T
ENST00000700184.1:n.375C>T
ENST00000700185.1:n.251C>T
ENST00000357654.9:c.132C>T
ENST00000471181.7:c.132C>T
ENST00000642945.1:c.132C>T
ENST00000644555.1:c.-10C>T
ENST00000652672.1:c.-10C>T
ENST00000352993.7:c.132C>T
ENST00000354071.7:c.132C>T
ENST00000357654.7:c.132C>T
ENST00000461221.5:c.132C>T
ENST00000461798.5:c.132C>T
ENST00000468300.5:c.132C>T
ENST00000470026.5:c.132C>T
ENST00000471181.6:c.132C>T
ENST00000476777.5:c.132C>T
ENST00000477152.5:c.132C>T
ENST00000478531.5:c.132C>T
ENST00000489037.1:c.132C>T
ENST00000491747.6:c.132C>T
ENST00000492859.5:c.132C>T
ENST00000493795.5:c.-8+8289C>T
ENST00000493919.5:c.-8+8289C>T
ENST00000494123.5:c.132C>T
ENST00000497488.1:c.-219+9543C>T
ENST00000586385.5:c.4+9454C>T
ENST00000591534.5:c.-44+9543C>T
ENST00000591849.5:c.-99+9543C>T
ENST00000634433.1:c.132C>T
NM_007294.3:c.132C>T
NM_007297.3:c.-8+8289C>T
NM_007298.3:c.132C>T
NM_007299.3:c.132C>T
NM_007300.3:c.132C>T
NR_027676.1:n.293C>T
NM_007297.4:c.-8+8289C>T
NM_007299.4:c.132C>T
NM_007300.4:c.132C>T
NR_027676.2:n.334C>T
More

Pathogenic

Met criteria codes 3
PS3 PM2_Supporting PVS1
Not Met criteria codes 1
PP3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
ENIGMA BRCA1 and BRCA2 VCEP
The c.132C>T variant in BRCA1 is a synonymous variant (p.(Cys44=)). This variant is absent from gnomAD v4.1 (read depth ≥25x in >90% samples, PM2_Supporting met). Silent variant, functional data considered only from assays that measure effect via mRNA and protein. Reported by one calibrated study incorporating mRNA splicing effects to exhibit function similar to pathogenic control variants (PMID:30209399) (PS3 met). This variant has a SpliceAI score of 0.92, predicting an impact on splicing (score threshold ≥0.2) (PP3 not applied because a PVS1 code is met). This variant is reported to result in aberrant mRNA splicing. Mini-gene demonstrated that the variant impacts splicing by usage of a cryptic splice donor site 4 bp within exon 3 resulting in a truncated protein. Sequencing of the gel bands showed the variant allele produced only the aberrant transcript (PMID: 24667779). A different Mini-gene assay confirmed the complete aberrant splicing. Non-allele specific RT-PCR on patient-derived mRNA (blood) also showed the aberrant splicing (skipping of 4 nucleotides) (PMID: 35087763). An additional assay in tumour tissue containing this variant produced the same aberrant transcript (PMID: 34120093). Appropriate code strength determined by comparison of results to PVS1 decision tree and Rubric of weighing mRNA data (Appendix Table 9): PVS1 (RNA). In summary, this variant meets the criteria to be classified as a Pathogenic variant for BRCA1-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (PM2_Supporting, PS3, PVS1 (RNA)).
Met criteria codes
PS3
Silent variant, functional data considered only from assays that measure effect via mRNA and protein. Reported by one calibrated study incorporating mRNA splicing effects to exhibit function similar to pathogenic control variants (PMID:30209399) (PS3 met).
PM2_Supporting
This variant is absent from gnomAD v4.1 (read depth ≥25x in >90% samples, PM2_Supporting met).
PVS1
This variant is reported to result in aberrant mRNA splicing. Mini-gene demonstrated that the variant impacts splicing by usage of a cryptic splice donor site 4 bp within exon 3 resulting in a truncated protein. Sequencing of the gel bands showed the variant allele produced only the aberrant transcript (PMID: 24667779). A different Mini-gene assay confirmed the complete aberrant splicing. Non-allele specific RT-PCR on patient-derived mRNA (blood) also showed the aberrant splicing (skipping of 4 nucleotides) (PMID: 35087763). An additional assay in tumour tissue containing this variant produced the same aberrant transcript (PMID: 34120093). Appropriate code strength determined by comparison of results to PVS1 decision tree and Rubric of weighing mRNA data (Appendix Table 9): PVS1 (RNA).
Not Met criteria codes
PP3
This variant has a SpliceAI score of 0.92, predicting an impact on splicing (score threshold ≥0.2) (PP3 not applied because a PVS1 code is met).
Curation History
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