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
  • No CSPEC computer assertion could be determined for this classification!


Variant: NM_007294.4(BRCA1):c.301+7G>A

CA001969

37499 (ClinVar)

Gene: BRCA1
Condition: BRCA1-related cancer predisposition
Inheritance Mode: Autosomal dominant inheritance
UUID: fbbb5452-b586-4a7b-9f6b-8416630042bc
Approved on: 2024-06-12
Published on: 2024-06-11

HGVS expressions

NM_007294.4:c.301+7G>A
NM_007294.4(BRCA1):c.301+7G>A
NC_000017.11:g.43104861C>T
CM000679.2:g.43104861C>T
NC_000017.10:g.41256878C>T
CM000679.1:g.41256878C>T
NC_000017.9:g.38510404C>T
NG_005905.2:g.113123G>A
ENST00000354071.8:n.365+7G>A
ENST00000461574.2:c.301+7G>A
ENST00000470026.6:c.301+7G>A
ENST00000473961.6:c.301+7G>A
ENST00000476777.6:c.301+7G>A
ENST00000477152.6:c.223+7G>A
ENST00000478531.6:c.301+7G>A
ENST00000489037.2:c.223+7G>A
ENST00000493919.6:c.160+7G>A
ENST00000494123.6:c.301+7G>A
ENST00000497488.2:c.-218-10001G>A
ENST00000618469.2:c.301+7G>A
ENST00000634433.2:c.301+7G>A
ENST00000644379.2:c.301+7G>A
ENST00000644555.2:c.160+7G>A
ENST00000652672.2:c.160+7G>A
ENST00000484087.6:c.301+7G>A
ENST00000700083.1:n.1272+7G>A
ENST00000700182.1:c.223+7G>A
ENST00000700183.1:c.*215+7G>A
ENST00000700184.1:n.544+7G>A
ENST00000357654.9:c.301+7G>A
ENST00000471181.7:c.301+7G>A
ENST00000642945.1:c.*175+7G>A
ENST00000644555.1:c.160+7G>A
ENST00000652672.1:c.160+7G>A
ENST00000352993.7:c.301+7G>A
ENST00000354071.7:c.301+7G>A
ENST00000357654.7:c.301+7G>A
ENST00000461221.5:c.*87+7G>A
ENST00000461798.5:c.*87+7G>A
ENST00000468300.5:c.301+7G>A
ENST00000470026.5:c.301+7G>A
ENST00000471181.6:c.301+7G>A
ENST00000473961.5:c.24+7G>A
ENST00000476777.5:c.301+7G>A
ENST00000477152.5:c.223+7G>A
ENST00000478531.5:c.301+7G>A
ENST00000484087.5:c.49+7G>A
ENST00000487825.5:c.49+7G>A
ENST00000489037.1:c.223+7G>A
ENST00000491747.6:c.301+7G>A
ENST00000492859.5:c.*237+7G>A
ENST00000493795.5:c.160+7G>A
ENST00000493919.5:c.160+7G>A
ENST00000494123.5:c.301+7G>A
ENST00000497488.1:c.-218-10001G>A
ENST00000586385.5:c.4+20321G>A
ENST00000591534.5:c.-44+20410G>A
ENST00000591849.5:c.-99+20410G>A
ENST00000634433.1:c.301+7G>A
NM_007294.3:c.301+7G>A
NM_007297.3:c.160+7G>A
NM_007298.3:c.301+7G>A
NM_007299.3:c.301+7G>A
NM_007300.3:c.301+7G>A
NR_027676.1:n.440+7G>A
NM_007297.4:c.160+7G>A
NM_007299.4:c.301+7G>A
NM_007300.4:c.301+7G>A
NR_027676.2:n.481+7G>A
More

Benign

Met criteria codes 4
BS1_Supporting BP7_Strong BP5_Strong BS3
Not Met criteria codes 1
PP3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen ENIGMA BRCA1 and BRCA2 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRCA1 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
ENIGMA BRCA1 and BRCA2 VCEP
The c.301+7G>A variant is an intronic variant occurring in intron 5 of the BRCA1 gene. The highest non-cancer, non-founder population filter allele frequency in gnomAD v2.1 (exomes only, non-cancer subset, read depth ≥20) or gnomAD v3.1 (non-cancer subset, read depth ≥20) is 0.00009711 in the European (non-Finnish) population which is within the ENIGMA BRCA1/2 VCEP threshold (>0.00002 to ≤ 0.0001) for BS1_Supporting (BS1_Supporting met). This BRCA1 intronic variant is located outside of the native donor and acceptor 1,2 splice sites, and the SpliceAI predictor score is 0.21, predicting an impact on splicing (score threshold >0.20) (however, this prediction is to strengthen the native acceptor site and therefore PP3 is not applied). This is an intronic variant, and mRNA experimental analysis indicates no impact on splicing (PMID: 22505045), considered strong evidence against pathogenicity (BP7_Strong (RNA)). Reported by one calibrated study to exhibit protein function similar to benign control variants (PMID: 30209399) (BS3 met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 4.848E-11 (based on Cosegregation LR=1.36; Pathology LR=0.001; Co-occurrence LR=0.068; Family History LR=0.037; Case-Control LR=1.28E-05), below the threshold for Very strong benign evidence (LR <0.00285) (BP5_Very strong met; PMID: 31131967). In summary, this variant meets the criteria to be classified as a Benign variant for BRCA1-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (BS1_Supporting, BP7_Strong (RNA), BS3, BP5_Very strong).
Met criteria codes
BS1_Supporting
The highest non-cancer, non-founder population filter allele frequency in gnomAD v2.1 (exomes only, non-cancer subset, read depth ≥20) or gnomAD v3.1 (non-cancer subset, read depth ≥20) is 0.00009711 in the European (non-Finnish) population which is within the ENIGMA BRCA1/2 VCEP threshold (>0.00002 to ≤ 0.0001) for BS1_Supporting (BS1_Supporting met).
BP7_Strong
This is an intronic variant, and mRNA experimental analysis indicates no impact on splicing (PMID: 22505045), considered strong evidence against pathogenicity (BP7_Strong (RNA)).
BP5_Strong
Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 4.848E-11 (based on Cosegregation LR=1.36; Pathology LR=0.001; Co-occurrence LR=0.068; Family History LR=0.037; Case-Control LR=1.28E-05), below the threshold for Very strong benign evidence (LR <0.00285) (BP5_Very strong met; PMID: 31131967).
BS3
Reported by one calibrated study to exhibit protein function similar to benign control variants (PMID: 30209399) (BS3 met).
Not Met criteria codes
PP3
This BRCA1 intronic variant is located outside of the native donor and acceptor 1,2 splice sites, and the SpliceAI predictor score is 0.21, predicting an impact on splicing (score threshold >0.20) (however, this prediction is to strengthen the native acceptor site and therefore PP3 is not applied).
Curation History
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