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 benign. Select a step to read what it means.
Likely benign.A likely benign 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.
No pathogenic criterion marked as applied in the recorded assessment.
This missense variant affects codon 221, which is outside the BRCA2 clinically important domains used by ENIGMA, and SpliceAI predicts no significant splice effect with a max delta score of 0.01, which is below the no-splicing threshold of 0.10. This supports BP1_Strong.
Expert panel ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen classified as Likely benign.
ENIGMA BRCA1/BRCA2 Specification v1.2 Table 3 final-classification framework (official CSPEC/VCEP framework; ACMG/AMP 2015 with ENIGMA Table 3 adaptations).
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 5 / 1,598,264 alleles. Recorded AF 3.12839e-06. Recorded homozygote count 0.
This variant is present in gnomAD v2.1 (AF= 4.08083e-06; MAF= 0.00041%, 1/245048 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 9.03228e-06; MAF= 0.00090%, 1/110714 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 has not reviewed this specific variant; no variant-level oncogenicity or biological effect is available. Gene-level context: BRCA2, a tumor suppressor involved in the DNA damage response, is mutated in various cancer types.
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: 2 met · 7 not met · 7 not assessed · 12 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
The BRCA2 c.663T>G (p.Phe221Leu, p.F221L) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar, where the ClinGen ENIGMA BRCA1/2 expert panel classified it as likely benign.
This variant is present at very low frequency in population databases, including gnomAD v2.1 at 1/245048 alleles (AF 4.08e-06) and gnomAD v4.1 at 5/1598264 alleles (AF 3.13e-06; grpmax FAF 4.45e-06), which is below ENIGMA BS1/BA1 thresholds and means the variant is not absent from controls for PM2_Supporting.
No calibrated ENIGMA functional assay result for this specific variant was identified in the curated BRCA2 functional dataset, so functional evidence was not applied.
This missense change occurs outside the BRCA2 PALB2-binding and DNA-binding domains used for ENIGMA missense protein interpretation, and SpliceAI predicts no significant splice effect with a maximum delta score of 0.01, supporting BP1_Strong.
No criteria match.
BP1_Strong applies to missense variants outside clinically important BRCA2 domains with no predicted splice impact (SpliceAI ≤0.10) under ENIGMA rules.
PS4 requires significant case-control enrichment with p-value ≤0.05 and OR ≥4 under the ENIGMA BRCA2 specification.
PM2_Supporting requires absence from gnomAD controls under the ENIGMA BRCA2 specification.
PP3 applies to qualifying domain missense variants with damaging protein prediction or to variants with SpliceAI ≥0.20 under ENIGMA BRCA2 rules.
PP4 applies only when the BRCA2 multifactorial clinical-history LR is ≥2.08 under ENIGMA rules.
BA1 requires FAF >0.001 in a non-founder population under ENIGMA BRCA2 rules.
BS1_Supporting requires FAF >0.00002 and BS1 requires FAF >0.0001 under ENIGMA BRCA2 rules.
BP5 applies only when the BRCA2 multifactorial clinical-history LR is ≤0.48 under ENIGMA rules.
PS1 applies when the same amino acid change, or the same splicing effect, is already established by a pathogenic or likely pathogenic variant under ENIGMA rules.
PS3 requires a calibrated damaging functional study for the specific variant under ENIGMA BRCA2 rules.
PM3 in BRCA2 is reserved for qualifying Fanconi anemia-related biallelic observations under ENIGMA rules.
PP1 requires a quantitative co-segregation likelihood ratio meeting ENIGMA thresholds.
BS2 in BRCA2 requires qualifying observations without Fanconi anemia features under ENIGMA rules.
BS3 requires a calibrated non-damaging functional study for the specific variant under ENIGMA BRCA2 rules.
BS4 requires a quantitative lack-of-segregation likelihood ratio meeting ENIGMA thresholds.
Apply PVS1 only to eligible null variants or qualifying RNA evidence under the ENIGMA BRCA2 specification.
PS2 is not applicable in the ENIGMA BRCA2 specification.
PM1 is not applicable in the ENIGMA BRCA2 specification.
PM4 is not applicable in the ENIGMA BRCA2 specification.
PM5 under the ENIGMA BRCA2 specification is applied as PM5_PTC for eligible protein-terminating variants.
PM6 is not applicable in the ENIGMA BRCA2 specification.
PP2 is not applicable in the ENIGMA BRCA2 specification.
PP5 is not applicable in the ENIGMA BRCA2 specification.
BP2 is not applicable in the ENIGMA BRCA2 specification.
BP3 is not applicable in the ENIGMA BRCA2 specification.
BP4 under ENIGMA BRCA2 is reserved for qualifying variants in specified domains or non-canonical intronic/silent settings.
BP7 under ENIGMA BRCA2 is applied in specific RNA-based synonymous, intronic, or qualifying missense settings.
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 |
|---|
| African/African American2 / 74,616 | 2.7e-05 |
| European (non-Finnish)3 / 1,167,478 | 2.6e-06 |
| European (non-Finnish)1 / 110,714 | 9e-06 |
This variant is present in gnomAD v4.1 (AF= 3.12839e-06; MAF= 0.00031%, 5/1598264 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 2.68039e-05; MAF= 0.00268%, 2/74616 alleles, homozygotes = 0); grpmax FAF= 4.45e-06.
This variant is present in gnomAD v2.1 (AF= 4.08083e-06; MAF= 0.00041%, 1/245048 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 9.03228e-06; MAF= 0.00090%, 1/110714 alleles, homozygotes = 0).
PP3 applies to qualifying domain missense variants with damaging protein prediction or to variants with SpliceAI ≥0.20 under ENIGMA BRCA2 rules.
BP4 under ENIGMA BRCA2 is reserved for qualifying variants in specified domains or non-canonical intronic/silent settings.
BP7 under ENIGMA BRCA2 is applied in specific RNA-based synonymous, intronic, or qualifying missense settings.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).
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= 3.12839e-06; MAF= 0.00031%, 5/1598264 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 2.68039e-05; MAF= 0.00268%, 2/74616 alleles, homozygotes = 0); grpmax FAF= 4.45e-06.
This variant is present in gnomAD v2.1 (AF= 4.08083e-06; MAF= 0.00041%, 1/245048 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 9.03228e-06; MAF= 0.00090%, 1/110714 alleles, homozygotes = 0).
This variant has been reported in ClinVar as Uncertain significance (8 clinical laboratories) and as Pathogenic (1 clinical laboratory) and as Uncertain Significance (1 clinical laboratory) and as Likely Benign 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 = 0.01).
OncoKB has not reviewed this specific variant; no variant-level oncogenicity or biological effect is available. Gene-level context: BRCA2, a tumor suppressor involved in the DNA damage response, is mutated in various cancer types.
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.