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 likely pathogenic. Select a step to read what it means.
Likely pathogenic.A likely 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.
In the ENIGMA BRCA2 curated functional dataset, this variant is assigned PS3 Strong because calibrated functional studies showed protein function similar to pathogenic control variants, supporting a damaging effect on BRCA2 function.
This missense variant lies within the BRCA2 DNA-binding functional region used by ENIGMA (amino acids 2481-3186) and has a BayesDel score of 0.575545, which is above the PP3 threshold of 0.30. REVEL is also high at 0.94, supporting a deleterious protein effect. SpliceAI predicts no significant splice impact (max delta score 0.00), so the computational evidence supports a damaging protein consequence rather than a splice mechanism.
Expert panel ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen classified as Pathogenic.
No benign criterion marked as applied in the recorded assessment.
ENIGMA BRCA1 and BRCA2 Specification v1.2.0 final-classification framework using Table 3 criteria-combination rules.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 6 / 1,614,162 alleles. Recorded AF 3.7171e-06. Recorded homozygote count 0.
This variant is present in gnomAD v2.1 (AF= 3.98251e-06; MAF= 0.00040%, 1/251098 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.81865e-06; MAF= 0.00088%, 1/113396 alleles, homozygotes = 0).
No SpliceAI or REVEL score is recorded in the fields used for this tile.
A ClinVar laboratory submission summary was not recorded.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Loss-of-function; curated oncogenicity label: Likely Oncogenic.
No COSMIC evidence statement is recorded in this case.
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: 3 met · 11 not met · 5 not assessed · 9 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
The BRCA2 c.8168A>C (p.Asp2723Ala, p.D2723A) variant has been reported in ClinVar and is classified as Pathogenic by the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel.
This variant is present at very low frequency in population databases, with 1/251098 alleles in gnomAD v2.1 (AF 3.98e-06) and 6/1614162 alleles in gnomAD v4.1 (AF 3.72e-06), which is too low to support a benign frequency criterion but means PM2 is not met because the variant is not absent from controls.
In the ENIGMA BRCA2 curated functional dataset, calibrated functional studies support PS3 Strong for this variant, indicating a damaging effect on BRCA2 function.
Computational evidence supports a damaging protein effect because the variant is in the BRCA2 DNA-binding region, BayesDel is 0.575545 above the PP3 threshold of 0.30, REVEL is 0.94, and SpliceAI predicts no significant splice impact (max delta score 0.00).
No criteria match.
ENIGMA BRCA2 PS3 uses calibrated functional studies with code strength assigned in Table 9.
ENIGMA BRCA2 PP3 applies to missense variants inside the defined functional domain with BayesDel >= 0.30, or to variants with predicted splice impact.
ENIGMA BRCA2 PVS1 applies to null variants or qualifying RNA loss-of-function evidence.
ENIGMA BRCA2 PS4 requires significant enrichment in affected individuals compared with controls.
ENIGMA BRCA2 PM2_Supporting requires absence from controls in gnomAD.
ENIGMA BRCA2 PP4 requires a clinical-history LR >= 2.08.
ENIGMA BRCA2 BA1 requires FAF > 0.1%.
ENIGMA BRCA2 BS1 uses FAF thresholds >0.00002 and >0.0001.
ENIGMA BRCA2 BS3 requires well-established studies showing no damaging effect.
ENIGMA BRCA2 BP1 applies to missense or silent variants outside the defined functional domains with no predicted splice effect.
ENIGMA BRCA2 BP4 requires no predicted impact by protein change or splicing.
ENIGMA BRCA2 BP5 requires a clinical-history LR <= 0.48.
ENIGMA BRCA2 BP7 is used for qualifying silent, intronic, or RNA-only benign splicing evidence scenarios.
ENIGMA BRCA2 PS1 requires the same amino acid substitution as an established pathogenic or likely pathogenic reference variant acting through protein change.
ENIGMA BRCA2 PM3 requires trans observations in BRCA2-related Fanconi anemia.
ENIGMA BRCA2 PP1 requires quantitative segregation evidence meeting LR thresholds.
ENIGMA BRCA2 BS2 requires point-based observations in the absence of Fanconi anemia features.
ENIGMA BRCA2 BS4 requires quantitative non-segregation evidence meeting LR thresholds.
Not applicable in ENIGMA BRCA2 specifications.
Not applicable as a standalone criterion in ENIGMA BRCA2.
Not applicable in ENIGMA BRCA2 specifications.
ENIGMA BRCA2 PM5 is configured as PM5_PTC for qualifying truncating variants.
Not applicable in ENIGMA BRCA2 specifications.
Not applicable in ENIGMA BRCA2 specifications.
Not applicable in ENIGMA BRCA2 specifications.
Not applicable in ENIGMA BRCA2 specifications.
Not applicable in ENIGMA BRCA2 specifications.
Every interpreted variant in BRCA2, mapped onto the exon structure of NM_000059.3. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| European (non-Finnish)6 / 1,180,024 | 5.1e-06 |
| European (non-Finnish)1 / 113,396 | 8.8e-06 |
This variant is present in gnomAD v4.1 (AF= 3.7171e-06; MAF= 0.00037%, 6/1614162 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.08464e-06; MAF= 0.00051%, 6/1180024 alleles, homozygotes = 0); grpmax FAF= 1.83e-06.
This variant is present in gnomAD v2.1 (AF= 3.98251e-06; MAF= 0.00040%, 1/251098 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.81865e-06; MAF= 0.00088%, 1/113396 alleles, homozygotes = 0).
ENIGMA BRCA2 PP3 applies to missense variants inside the defined functional domain with BayesDel >= 0.30, or to variants with predicted splice impact.
ENIGMA BRCA2 BP4 requires no predicted impact by protein change or splicing.
ENIGMA BRCA2 BP7 is used for qualifying silent, intronic, or RNA-only benign splicing evidence scenarios.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.94. BayesDel score = 0.575545.
0 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata.
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= 3.7171e-06; MAF= 0.00037%, 6/1614162 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.08464e-06; MAF= 0.00051%, 6/1180024 alleles, homozygotes = 0); grpmax FAF= 1.83e-06.
This variant is present in gnomAD v2.1 (AF= 3.98251e-06; MAF= 0.00040%, 1/251098 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.81865e-06; MAF= 0.00088%, 1/113396 alleles, homozygotes = 0).
This variant has been reported in ClinVar as Likely pathogenic (4 clinical laboratories) and as Uncertain significance (1 clinical laboratory) and as Likely Pathogenic (1 clinical laboratory) and as Pathogenic (1 clinical laboratory) and as Pathogenic by ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen (expert panel).
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.94. BayesDel score = 0.575545.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Loss-of-function; curated oncogenicity label: Likely Oncogenic.
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.