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.212+3A>G

CA001412

54467 (ClinVar)

Gene: BRCA1
Condition: BRCA1-related cancer predisposition
Inheritance Mode: Autosomal dominant inheritance
UUID: b2402846-e923-4f48-9ac2-a6a097c7e175
Approved on: 2024-06-12
Published on: 2024-06-11

HGVS expressions

NM_007294.4:c.212+3A>G
NM_007294.4(BRCA1):c.212+3A>G
NC_000017.11:g.43106453T>C
CM000679.2:g.43106453T>C
NC_000017.10:g.41258470T>C
CM000679.1:g.41258470T>C
NC_000017.9:g.38511996T>C
NG_005905.2:g.111531A>G
ENST00000354071.8:n.276+3A>G
ENST00000461574.2:c.212+3A>G
ENST00000470026.6:c.212+3A>G
ENST00000473961.6:c.212+3A>G
ENST00000476777.6:c.212+3A>G
ENST00000477152.6:c.135-1497A>G
ENST00000478531.6:c.212+3A>G
ENST00000489037.2:c.135-1497A>G
ENST00000493919.6:c.71+3A>G
ENST00000494123.6:c.212+3A>G
ENST00000497488.2:c.-218-11593A>G
ENST00000618469.2:c.212+3A>G
ENST00000634433.2:c.212+3A>G
ENST00000644379.2:c.212+3A>G
ENST00000644555.2:c.71+3A>G
ENST00000652672.2:c.71+3A>G
ENST00000484087.6:c.212+3A>G
ENST00000700182.1:c.135-1497A>G
ENST00000700183.1:c.*126+25A>G
ENST00000700184.1:n.455+3A>G
ENST00000357654.9:c.212+3A>G
ENST00000471181.7:c.212+3A>G
ENST00000642945.1:c.*86+3A>G
ENST00000644555.1:c.71+3A>G
ENST00000652672.1:c.71+3A>G
ENST00000352993.7:c.212+3A>G
ENST00000354071.7:c.212+3A>G
ENST00000357654.7:c.212+3A>G
ENST00000461221.5:c.190+25A>G
ENST00000461798.5:c.190+25A>G
ENST00000468300.5:c.212+3A>G
ENST00000470026.5:c.212+3A>G
ENST00000471181.6:c.212+3A>G
ENST00000476777.5:c.212+3A>G
ENST00000477152.5:c.135-1497A>G
ENST00000478531.5:c.212+3A>G
ENST00000489037.1:c.135-1497A>G
ENST00000491747.6:c.212+3A>G
ENST00000492859.5:c.*148+3A>G
ENST00000493795.5:c.71+3A>G
ENST00000493919.5:c.71+3A>G
ENST00000494123.5:c.212+3A>G
ENST00000497488.1:c.-218-11593A>G
ENST00000586385.5:c.4+18729A>G
ENST00000591534.5:c.-44+18818A>G
ENST00000591849.5:c.-99+18818A>G
ENST00000634433.1:c.212+3A>G
NM_007294.3:c.212+3A>G
NM_007297.3:c.71+3A>G
NM_007298.3:c.212+3A>G
NM_007299.3:c.212+3A>G
NM_007300.3:c.212+3A>G
NR_027676.1:n.351+25A>G
NM_007297.4:c.71+3A>G
NM_007299.4:c.212+3A>G
NM_007300.4:c.212+3A>G
NR_027676.2:n.392+25A>G
More

Pathogenic

Met criteria codes 3
PVS1 PS3 PP4_Strong
Not Met criteria codes 3
BA1 BS1 PM2

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.212+3A>G variant is an intronic variant occurring in intron 4 of the BRCA1 gene. This variant is present in gnomAD v2.1 (exomes only, non-cancer subset) or gnomAD v3.1 (non-cancer subset) but is below the ENIGMA BRCA1/2 VCEP threshold >0.00002 for BS1_Supporting (PM2_Supporting, BS1, and BA1 are not met). This variant is reported to result in aberrant mRNA splicing. A combination of RT-PCR from patient samples and mini-gene assays demonstrated that the variant impacts splicing by skipping of 22nt from the 3' end of the exon, reported by five studies (PMIDs: 22505045, 11802209, 20215541, 21673748, 24667779). Two of these studies also reported skipping of exon 4 (PMIDs: 20215541, 24667779). Allele-specific expression was reported by one assay on patient-derived material (PMID: 22505045), which showed no WT transcript from the variant allele. This is in agreement with two minigene assays (PMIDs: 21673748, 24667779). One study reported no impact on splicing but no results are shown to assess whether the 22nt skipping event (that is seen in controls at low level) was increased (PMID: 16619214), and therefore, has been excluded from consideration when assessing the splicing impact of this variant. Appropriate code strength determined by comparison of results to PVS1 decision tree (PVS1 (RNA) met). Reported by one calibrated study to exhibit protein function similar to pathogenic control variants (PMID: 30209399) (PS3 met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 1615.48 (based on Co-occurrence LR=1.298; Family History LR=1245.06), above the threshold for Very strong evidence towards pathogenicity (LR >350) (PP4_Very strong met; PMID: 17924331, 31853058). 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 (PVS1 (RNA), PS3, PP4_Very strong).
Met criteria codes
PVS1
This variant is reported to result in aberrant mRNA splicing. A combination of RT-PCR from patient samples and mini-gene assays demonstrated that the variant impacts splicing by skipping of 22nt from the 3' end of the exon, reported by five studies (PMIDs: 22505045, 11802209, 20215541, 21673748, 24667779). Two of these studies also reported skipping of exon 4 (PMIDs: 20215541, 24667779). Allele-specific expression was reported by one assay on patient-derived material (PMID: 22505045), which showed no WT transcript from the variant allele. This is in agreement with two minigene assays (PMIDs: 21673748, 24667779). One study reported no impact on splicing but no results are shown to assess whether the 22nt skipping event (that is seen in controls at low level) was increased (PMID: 16619214), and therefore, has been excluded from consideration when assessing the splicing impact of this variant. Appropriate code strength determined by comparison of results to PVS1 decision tree (PVS1 (RNA) met).
PS3
Reported by one calibrated study to exhibit protein function similar to pathogenic control variants (PMID: 30209399) (PS3 met).
PP4_Strong
Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 1615.48 (based on Co-occurrence LR=1.298; Family History LR=1245.06), above the threshold for Very strong evidence towards pathogenicity (LR >350) (PP4_Very strong met; PMID: 17924331).
Not Met criteria codes
BA1
This variant is present in gnomAD v2.1 (exomes only, non-cancer subset) or gnomAD v3.1 (non-cancer subset) but is below the ENIGMA BRCA1/2 VCEP threshold >0.00002 for BS1_Supporting (PM2_Supporting, BS1, and BA1 are not met).
BS1
This variant is present in gnomAD v2.1 (exomes only, non-cancer subset) or gnomAD v3.1 (non-cancer subset) but is below the ENIGMA BRCA1/2 VCEP threshold >0.00002 for BS1_Supporting (PM2_Supporting, BS1, and BA1 are not met).
PM2
This variant is present in gnomAD v2.1 (exomes only, non-cancer subset) or gnomAD v3.1 (non-cancer subset) but is below the ENIGMA BRCA1/2 VCEP threshold >0.00002 for BS1_Supporting (PM2_Supporting, BS1, and BA1 are not met).
Curation History
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