About BRCA2
No gene-level summary was recorded for this case.
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is pathogenic. Select a step to read what it means.
Pathogenic.A pathogenic classification under the recorded framework.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.No gene-level summary was recorded for this case.
The recorded framework is ClinGen BRCA2 VCEP v1.2.0. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
This variant is a frameshift deletion predicted to produce p.(Asn1784HisfsTer2), truncating BRCA2 shortly after codon 1784. In the ENIGMA BRCA2 specification, loss of function is an established disease mechanism, and exon 11 is designated as PVS1-applicable; therefore full-strength PVS1 is met.
In the BRCA2 ENIGMA framework, PM5 is repurposed for truncating variants. This frameshift creates a premature termination codon in exon 11, and ENIGMA Table 4 assigns exon 11 a PM5_Strong (PTC) designation, so PM5 is met at Strong strength.
This variant has a BRCA2 clinical-history likelihood ratio of 812.95 based on 42 probands in the ENIGMA-supported Li et al. dataset. This value is above the Very Strong threshold of 350, so PP4 is met at Very Strong strength.
Expert panel Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) classified as Pathogenic.
No benign criterion marked as applied in the recorded assessment.
ENIGMA BRCA1 and BRCA2 Specification v1.2.0 Table 3 criteria-combination framework (CSPEC/VCEP official framework override).
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 41 / 1,612,540 alleles. Recorded AF 2.54257e-05. Recorded homozygote count 0.
This variant is present in gnomAD v2.1 (AF= 3.20533e-05; MAF= 0.00321%, 1/31198 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 6.52912e-05; MAF= 0.00653%, 1/15316 alleles, homozygotes = 0).
Absent from gnomAD-Canada v1.0.
Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.
35 Pathogenic · 1 Uncertain significance.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
This variant has previously been reported in somatic cancers (COSMIC; COSV104701329, n = 1 times).
This variant does not lie in a statistically significant hotspot.
ACMG/AMP criteria under ClinGen BRCA2 VCEP v1.2.0, with the data and sources behind each one.
28 criteria with recorded statuses: 4 met · 4 not met · 7 not assessed · 13 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
The BRCA2 NM_000059.4:c.5350_5351del (NP_000050.3:p.(Asn1784HisfsTer2); p.(N1784Hfs*2)) variant has been reported in ClinVar with an expert-panel Pathogenic classification, and curated somatic review resources describe it as a likely loss-of-function BRCA2 alteration.
This variant is present in population databases at low frequency, including 1/31,198 alleles in gnomAD v2.1 (AF 3.20533e-05) and 41/1,612,540 alleles in gnomAD v4.1 (AF 2.54257e-05; grpmax FAF 2.315e-05), which is too high for PM2 but far below BA1.
The variant is a frameshift deletion predicted to truncate BRCA2 after codon 1784, and the ENIGMA BRCA2 exon-level table designates exon 11 as eligible for full-strength PVS1 and PM5_Strong (PTC).
Clinical-history modeling for BRCA2 reports a likelihood ratio of 812.95 from 42 probands, exceeding the ENIGMA Very Strong PP4 threshold of 350; SpliceAI shows no separate splice signal (max delta 0.00).
No criteria match.
ENIGMA BRCA2 PVS1 for null variants in a gene with established loss-of-function mechanism; exon 11 is PVS1-applicable.
ENIGMA BRCA2 PM5_PTC applies to qualifying truncating variants by exon-level assignment in Table 4.
ENIGMA PP4_VeryStrong for combined clinical-history LR ≥350.
ENIGMA PM2_Supporting requires absence from controls in gnomAD.
ENIGMA BA1 requires FAF >0.1% in the specified population dataset.
ENIGMA BS1 requires qualifying FAF above benign thresholds.
ENIGMA BP5 applies only when combined clinical likelihood ratios support a benign direction.
Apply PS3 only from variant-specific well-established functional evidence under ENIGMA Table 9/Figure 1C.
ENIGMA PM3 applies only to qualifying recessive Fanconi anemia observations.
ENIGMA PP1 requires quantitative co-segregation likelihood ratios.
ENIGMA BS2 requires specific point-based observations in the absence of recessive disease features.
Apply BS3 only from variant-specific well-established benign functional evidence under ENIGMA Table 9/Figure 1C.
ENIGMA BS4 requires quantitative lack-of-segregation evidence.
ENIGMA PS1 applies to qualifying missense or same-splice-effect comparisons.
Criterion marked not applicable in ENIGMA BRCA2 specification.
Criterion marked not applicable in ENIGMA BRCA2 specification.
Criterion marked not applicable in ENIGMA BRCA2 specification.
Criterion marked not applicable in ENIGMA BRCA2 specification.
Criterion marked not applicable in ENIGMA BRCA2 specification.
ENIGMA PP3 applies to specified missense/in-frame/splicing contexts, not to this frameshift truncating variant.
ENIGMA BP1 applies only to specified non-truncating variant classes.
Criterion marked not applicable in ENIGMA BRCA2 specification.
Criterion marked not applicable in ENIGMA BRCA2 specification.
ENIGMA BP4 applies only to specified non-truncating variant classes.
Criterion marked not applicable in ENIGMA BRCA2 specification.
ENIGMA BP7 applies only to specified silent/intronic or RNA-only contexts.
Every interpreted variant in BRCA2, mapped onto the exon structure of NM_000059.4. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| Remaining individuals3 / 62,434 | 4.8e-05 |
| European (non-Finnish)37 / 1,179,132 | 3.1e-05 |
| African/African American1 / 74,774 | 1.3e-05 |
| European (non-Finnish)1 / 15,316 | 6.5e-05 |
This variant is present in gnomAD v4.1 (AF= 2.54257e-05; MAF= 0.00254%, 41/1612540 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 4.80507e-05; MAF= 0.00481%, 3/62434 alleles, homozygotes = 0); grpmax FAF= 2.315e-05.
This variant is present in gnomAD v2.1 (AF= 3.20533e-05; MAF= 0.00321%, 1/31198 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 6.52912e-05; MAF= 0.00653%, 1/15316 alleles, homozygotes = 0).
Absent from gnomAD-Canada v1.0.
ENIGMA PP3 applies to specified missense/in-frame/splicing contexts, not to this frameshift truncating variant.
ENIGMA BP4 applies only to specified non-truncating variant classes.
ENIGMA BP7 applies only to specified silent/intronic or RNA-only contexts.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
9 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
This variant is present in gnomAD v4.1 (AF= 2.54257e-05; MAF= 0.00254%, 41/1612540 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 4.80507e-05; MAF= 0.00481%, 3/62434 alleles, homozygotes = 0); grpmax FAF= 2.315e-05.
This variant is present in gnomAD v2.1 (AF= 3.20533e-05; MAF= 0.00321%, 1/31198 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 6.52912e-05; MAF= 0.00653%, 1/15316 alleles, homozygotes = 0).
Absent from gnomAD-Canada v1.0.
This variant has been reported in ClinVar as Pathogenic (35 clinical laboratories) and as Uncertain significance (1 clinical laboratory) and as Pathogenic by Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) (expert panel). (ClinVarID = 37959)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV104701329, n = 1 times).
This variant does not lie in a statistically significant hotspot.