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Variant interpretation report

BRCA2 c.663T>G, p.(Phe221Leu)

NM_000059.4:c.663T>G NP_000050.3:p.(Phe221Leu) View identifiers
Classification
Likely benign

Variant description:

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.

In plain language

Gene-level background from the recorded interpretation.

About BRCA2

No gene-level summary was recorded for this case.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
01The reasoning

How it was classified

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.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 0 Benign evidence criteria: 2
Pathogenic criteria applied · 0

No pathogenic criterion marked as applied in the recorded assessment.

Benign criteria applied · 2
BP1Strong
BP1 · strong

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.

BP6Supporting
BP6 · supporting

Expert panel ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen classified as Likely benign.

Recorded classification: 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).

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

gnomAD v4.1
gnomAD v2.1
Population frequency
5 / 1,598,264 alleles

gnomAD v4.1: 5 / 1,598,264 alleles. Recorded AF 3.12839e-06. Recorded homozygote count 0.

gnomAD v2.1

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 listed criterion applied
No screenshot for this evidence
Computational predictions
Not recorded

No SpliceAI or REVEL score is recorded in the fields used for this tile.

No listed criterion applied
Functional evidence
Statement 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 listed criterion applied OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
Not assessed

No COSMIC evidence statement is recorded in this case.

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.

For specialists

Technical detail

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.

Met Not met Not assessed Not applicable

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.

Met · 2

BP1 StrongThis 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. Details ▾Hide ▴
Rule
BP1_Strong applies to missense variants outside clinically important BRCA2 domains with no predicted splice impact (SpliceAI ≤0.10) under ENIGMA rules.
Evidence considered
  • Protein position 221 is outside the BRCA2 PALB2-binding domain (aa 10-40) and DNA-binding region (aa 2481-3186).
  • SpliceAI max delta score = 0.01
  • below the ≤0.10 threshold.
Sources
BP6 SupportingExpert panel ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen classified as Likely benign. Details ▾Hide ▴
Rule
BP6 is not applicable in the ENIGMA BRCA2 specification.
Evidence considered
  • ENIGMA BRCA2 specification marks BP6 as not applicable.
  • ClinVar expert panel classification
Sources

Not met · 7 · evaluated, threshold not reached

PS4 Available evidence does not show a statistically significant enrichment of this variant in affected individuals compared with controls. No case-control result meeting the ENIGMA PS4 threshold of p-value ≤0.05 and odds ratio ≥4 was identified. Details ▾Hide ▴
Rule
PS4 requires significant case-control enrichment with p-value ≤0.05 and OR ≥4 under the ENIGMA BRCA2 specification.
Evidence considered
  • Parsons et al. structured dataset lists the variant but does not provide a qualifying case-control likelihood ratio or a case-control result meeting ENIGMA PS4 requirements.
Sources
cspec ↗vcep_humu_40_1557_s001PMID:31131967 ↗
PM2 This variant is not absent from population databases. It is present in gnomAD v2.1 at 1/245048 alleles (AF 4.08e-06) and in gnomAD v4.1 at 5/1598264 alleles (AF 3.13e-06), so it does not meet the ENIGMA PM2_Supporting requirement for absence from controls. Details ▾Hide ▴
Rule
PM2_Supporting requires absence from gnomAD controls under the ENIGMA BRCA2 specification.
Evidence considered
  • gnomAD v2.1: 1/245048 alleles
  • AF 4.08083e-06.
  • gnomAD v4.1: 5/1598264 alleles
  • AF 3.12839e-06.
Sources
PP3 Available predictive evidence does not support PP3. This missense variant lies outside the BRCA2 clinically important domains used for PP3 protein-based application, and SpliceAI predicts no significant splice effect with a max delta score of 0.01, which is below the ENIGMA PP3 splice threshold of 0.20. Details ▾Hide ▴
Rule
PP3 applies to qualifying domain missense variants with damaging protein prediction or to variants with SpliceAI ≥0.20 under ENIGMA BRCA2 rules.
Evidence considered
  • Protein position 221 is outside the BRCA2 PALB2-binding domain (aa 10-40) and DNA-binding region (aa 2481-3186).
  • SpliceAI max delta score = 0.01.
Sources
PP4 The BRCA2 clinical-history likelihood ratio for this variant is 0.67 in 6 probands, which is below the ENIGMA PP4 threshold of 2.08. Available evidence therefore does not support PP4. Details ▾Hide ▴
Rule
PP4 applies only when the BRCA2 multifactorial clinical-history LR is ≥2.08 under ENIGMA rules.
Evidence considered
  • Li et al. 2020 BRCA2 clinical-history LR = 0.6735279240 for c.663T>G in 6 probands.
Sources
cspec ↗vcep_pmid_31853058_brca2_clinical_history_lrPMID:31853058 ↗
BA1 This variant does not reach the ENIGMA BA1 threshold. The highest available group maximum filtering allele frequency is 4.45e-06 in gnomAD v4.1, which is below the BA1 threshold of 0.001. Details ▾Hide ▴
Rule
BA1 requires FAF >0.001 in a non-founder population under ENIGMA BRCA2 rules.
Evidence considered
  • gnomAD v4.1 grpmax FAF = 4.45e-06.
  • gnomAD v2.1 total AF = 4.08083e-06.
Sources
BS1 Population frequency is below the ENIGMA BS1 thresholds. The highest available group maximum filtering allele frequency is 4.45e-06 in gnomAD v4.1, which is below the BS1_Supporting threshold of 0.00002 and the BS1 threshold of 0.0001, so BS1 is not met. Details ▾Hide ▴
Rule
BS1_Supporting requires FAF >0.00002 and BS1 requires FAF >0.0001 under ENIGMA BRCA2 rules.
Evidence considered
  • gnomAD v4.1 grpmax FAF = 4.45e-06.
  • gnomAD v2.1 total AF = 4.08083e-06.
Sources
BP5 The BRCA2 clinical-history likelihood ratio for this variant is 0.67 in 6 probands, which is above the ENIGMA BP5 threshold of 0.48. This value is in the neutral zone, so BP5 is not met. Details ▾Hide ▴
Rule
BP5 applies only when the BRCA2 multifactorial clinical-history LR is ≤0.48 under ENIGMA rules.
Evidence considered
  • Li et al. 2020 BRCA2 clinical-history LR = 0.6735279240 for c.663T>G in 6 probands.
Sources
cspec ↗vcep_pmid_31853058_brca2_clinical_history_lrPMID:31853058 ↗

Not assessed · 7 · no assessment recorded

PS1 No same-amino-acid pathogenic or likely pathogenic BRCA2 variant acting through the same predicted mechanism was identified from the available evidence, so PS1 was not assessed. Details ▾Hide ▴
Rule
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.
Evidence considered
  • ClinVar contains multiple submissions for c.663T>G itself
  • but the available evidence does not identify a different pathogenic or likely pathogenic variant producing the same amino acid change.
  • SpliceAI predicts no significant splice effect (max delta score 0.01).
Still missing
  • A dedicated same-amino-acid comparison dataset was not identified in the available materials.
Sources
PS3 No calibrated BRCA2 functional assay result for this specific variant was identified in the curated ENIGMA functional dataset, so PS3 was not assessed. Details ▾Hide ▴
Rule
PS3 requires a calibrated damaging functional study for the specific variant under ENIGMA BRCA2 rules.
Evidence considered
  • No direct entry for c.663T>G / p.(Phe221Leu) was identified in ENIGMA Table 9.
Still missing
  • A validated damaging functional assay result for c.663T>G was not identified.
Sources
cspec ↗vcep_specifications_table9_v1_2_2024_11_18
PM3 No evidence was identified for biallelic BRCA2 disease, Fanconi anemia phenotype, or qualifying trans observations for this variant, so PM3 was not assessed. Details ▾Hide ▴
Rule
PM3 in BRCA2 is reserved for qualifying Fanconi anemia-related biallelic observations under ENIGMA rules.
Evidence considered
  • Available materials do not provide PM3 point-based evidence for BRCA2-related Fanconi anemia.
Still missing
  • No proband-level Fanconi anemia phenotype or trans co-occurrence data were identified.
Sources
PP1 No quantitative co-segregation result was identified for this variant, so PP1 was not assessed. Details ▾Hide ▴
Rule
PP1 requires a quantitative co-segregation likelihood ratio meeting ENIGMA thresholds.
Evidence considered
  • The structured Parsons dataset does not provide a segregation LR for c.663T>G.
Still missing
  • No family-based segregation likelihood ratio was identified.
Sources
cspec ↗vcep_humu_40_1557_s001
BS2 No point-based evidence was identified showing this variant in individuals without features of BRCA2-related Fanconi anemia, so BS2 was not assessed. Details ▾Hide ▴
Rule
BS2 in BRCA2 requires qualifying observations without Fanconi anemia features under ENIGMA rules.
Evidence considered
  • Available materials do not provide BS2 point assignments for this variant.
Still missing
  • No qualifying BS2 proband data were identified.
Sources
BS3 No calibrated benign functional assay result for this specific variant was identified in the curated ENIGMA functional dataset, so BS3 was not assessed. Details ▾Hide ▴
Rule
BS3 requires a calibrated non-damaging functional study for the specific variant under ENIGMA BRCA2 rules.
Evidence considered
  • No direct entry for c.663T>G / p.(Phe221Leu) was identified in ENIGMA Table 9.
Still missing
  • A validated non-damaging functional assay result for c.663T>G was not identified.
Sources
cspec ↗vcep_specifications_table9_v1_2_2024_11_18
BS4 No quantitative lack-of-segregation likelihood ratio was identified for this variant, so BS4 was not assessed. Details ▾Hide ▴
Rule
BS4 requires a quantitative lack-of-segregation likelihood ratio meeting ENIGMA thresholds.
Evidence considered
  • The structured Parsons dataset does not provide a segregation LR for c.663T>G.
Still missing
  • No family-based lack-of-segregation likelihood ratio was identified.
Sources
cspec ↗vcep_humu_40_1557_s001
Not applicable · 12· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/AThis missense variant, NM_000059.4:c.663T>G (p.Phe221Leu, p.F221L), does not fall into the BRCA2 PVS1 null-variant categories, and no RNA study demonstrating a pathogenic transcript effect was identified. Available evidence therefore does not support application of PVS1. Details ▾Hide ▴
Rule
Apply PVS1 only to eligible null variants or qualifying RNA evidence under the ENIGMA BRCA2 specification.
Evidence considered
  • BRCA2 loss of function is an established disease mechanism in the ENIGMA BRCA2 framework.
  • Variant-level PVS1 scaffold states this variant is not a nonsense
  • frameshift
  • or canonical ±1
  • 2 splice variant.
Still missing
  • RNA assay data demonstrating a pathogenic transcript effect were not identified.
Sources
cspec ↗pvs1_gene_contextpvs1_variant_assessment
PS2 N/ADe novo evidence is not part of the ENIGMA BRCA2 framework for this review, so PS2 is not applicable. Details ▾Hide ▴
Rule
PS2 is not applicable in the ENIGMA BRCA2 specification.
Evidence considered
  • ENIGMA BRCA2 specification marks PS2 as not applicable.
Sources
PM1 N/APM1 is not applicable in the ENIGMA BRCA2 specification. Details ▾Hide ▴
Rule
PM1 is not applicable in the ENIGMA BRCA2 specification.
Evidence considered
  • ENIGMA BRCA2 specification marks PM1 as not applicable.
Sources
PM4 N/APM4 is not applicable in the ENIGMA BRCA2 specification. Details ▾Hide ▴
Rule
PM4 is not applicable in the ENIGMA BRCA2 specification.
Evidence considered
  • ENIGMA BRCA2 specification marks PM4 as not applicable.
Sources
PM5 N/AIn the ENIGMA BRCA2 specification, PM5 is used for protein-terminating variants in eligible exons. This variant is missense, so PM5 is not applicable. Details ▾Hide ▴
Rule
PM5 under the ENIGMA BRCA2 specification is applied as PM5_PTC for eligible protein-terminating variants.
Evidence considered
  • ENIGMA Table 4 defines PM5_PTC for protein-terminating variants rather than missense substitutions.
Sources
cspec ↗vcep_specifications_table4_v1_2_2024_11_18
PM6 N/APM6 is not applicable in the ENIGMA BRCA2 specification. Details ▾Hide ▴
Rule
PM6 is not applicable in the ENIGMA BRCA2 specification.
Evidence considered
  • ENIGMA BRCA2 specification marks PM6 as not applicable.
Sources
PP2 N/APP2 is not applicable in the ENIGMA BRCA2 specification. Details ▾Hide ▴
Rule
PP2 is not applicable in the ENIGMA BRCA2 specification.
Evidence considered
  • ENIGMA BRCA2 specification marks PP2 as not applicable.
Sources
PP5 N/APP5 is not applicable in the ENIGMA BRCA2 specification. Details ▾Hide ▴
Rule
PP5 is not applicable in the ENIGMA BRCA2 specification.
Evidence considered
  • ENIGMA BRCA2 specification marks PP5 as not applicable.
Sources
BP2 N/ABP2 is not applicable in the ENIGMA BRCA2 specification. Details ▾Hide ▴
Rule
BP2 is not applicable in the ENIGMA BRCA2 specification.
Evidence considered
  • ENIGMA BRCA2 specification marks BP2 as not applicable.
Sources
BP3 N/ABP3 is not applicable in the ENIGMA BRCA2 specification. Details ▾Hide ▴
Rule
BP3 is not applicable in the ENIGMA BRCA2 specification.
Evidence considered
  • ENIGMA BRCA2 specification marks BP3 as not applicable.
Sources
BP4 N/AFor BRCA2 missense variants, the ENIGMA BP4 protein-based rule is used for variants inside clinically important domains with benign predictions. This variant is outside those domains, so BP4 is not the appropriate rule for this observation and BP1_Strong is used instead. Details ▾Hide ▴
Rule
BP4 under ENIGMA BRCA2 is reserved for qualifying variants in specified domains or non-canonical intronic/silent settings.
Evidence considered
  • Protein position 221 is outside the BRCA2 PALB2-binding domain (aa 10-40) and DNA-binding region (aa 2481-3186).
  • SpliceAI max delta score = 0.01.
Sources
BP7 N/AThis is a missense variant rather than a synonymous or qualifying intronic variant, so BP7 is not applicable. Details ▾Hide ▴
Rule
BP7 under ENIGMA BRCA2 is applied in specific RNA-based synonymous, intronic, or qualifying missense settings.
Evidence considered
  • ENIGMA BP7 rules are defined for RNA-based evidence in synonymous
  • intronic
  • and limited missense contexts not met here.
Sources

Identifiers

Gene
BRCA2
Transcript
NM_000059.4
Coding (HGVS c.)
NM_000059.4:c.663T>G
Protein (HGVS p.)
NP_000050.3:p.(Phe221Leu)
GRCh38
chr13:32329474 T>G
GRCh37
chr13:32903611 T>G

Gene diagram

Every interpreted variant in BRCA2, mapped onto the exon structure of NM_000059.4. Select a row to find it on the plot.

BRCA2NM_000059.4
Fetching transcript structure from UCSC…
gnomAD v4.1 5 / 1,598,264 alleles AF 3.13e-06 · 0 homozygotes · FAF 4.45e-06
gnomAD v2.1 1 / 245,048 alleles AF 4.08e-06 · 0 homozygotes

By genetic ancestry

gnomAD v4.1

AF 3.1e-06 · 5 / 1,598,264 alleles · 0 hom · FAF 4.4e-06
African/African American2 / 74,616 2.7e-05
European (non-Finnish)3 / 1,167,478 2.6e-06
0 alternate alleles recorded in 8 other groups: Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish.

gnomAD v2.1

AF 4.1e-06 · 1 / 245,048 alleles · 0 hom
European (non-Finnish)1 / 110,714 9e-06
0 alternate alleles recorded in 7 other groups: African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian.

Statements

gnomAD v4.1

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.

gnomAD v2.1

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).

Other predictors

REVEL
Not available
BayesDel
Not available

How the predictions were used

PP3 Available predictive evidence does not support PP3. This missense variant lies outside the BRCA2 clinically important domains used for PP3 protein-based application, and SpliceAI predicts no significant splice effect with a max delta score of 0.01, which is below the ENIGMA PP3 splice threshold of 0.20. Details ▾Hide ▴
Rule
PP3 applies to qualifying domain missense variants with damaging protein prediction or to variants with SpliceAI ≥0.20 under ENIGMA BRCA2 rules.
Evidence considered
  • Protein position 221 is outside the BRCA2 PALB2-binding domain (aa 10-40) and DNA-binding region (aa 2481-3186).
  • SpliceAI max delta score = 0.01.
Sources
BP4 N/AFor BRCA2 missense variants, the ENIGMA BP4 protein-based rule is used for variants inside clinically important domains with benign predictions. This variant is outside those domains, so BP4 is not the appropriate rule for this observation and BP1_Strong is used instead. Details ▾Hide ▴
Rule
BP4 under ENIGMA BRCA2 is reserved for qualifying variants in specified domains or non-canonical intronic/silent settings.
Evidence considered
  • Protein position 221 is outside the BRCA2 PALB2-binding domain (aa 10-40) and DNA-binding region (aa 2481-3186).
  • SpliceAI max delta score = 0.01.
Sources
BP7 N/AThis is a missense variant rather than a synonymous or qualifying intronic variant, so BP7 is not applicable. Details ▾Hide ▴
Rule
BP7 under ENIGMA BRCA2 is applied in specific RNA-based synonymous, intronic, or qualifying missense settings.
Evidence considered
  • ENIGMA BP7 rules are defined for RNA-based evidence in synonymous
  • intronic
  • and limited missense contexts not met here.
Sources

Statement

In silico

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.

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

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.

gnomAD v2.1

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).

ClinVar

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).

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).

Functional

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.

Somatic

This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.