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Variant interpretation report

BRCA2 c.8168A>C, p.(Asp2723Ala)

NM_000059.3:c.8168A>C NP_000050.2:p.(Asp2723Ala) View identifiers
Classification
Likely pathogenic

Variant description:

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.

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: 3 Benign evidence criteria: 0
Pathogenic criteria applied · 3
PS3Strong
PS3 · strong

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.

PP3Supporting
PP3 · supporting

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.

PP5Supporting
PP5 · supporting

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

Benign criteria applied · 0

No benign criterion marked as applied in the recorded assessment.

Recorded classification: Likely pathogenic

ENIGMA BRCA1 and BRCA2 Specification v1.2.0 final-classification framework using Table 3 criteria-combination rules.

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
6 / 1,614,162 alleles

gnomAD v4.1: 6 / 1,614,162 alleles. Recorded AF 3.7171e-06. Recorded homozygote count 0.

gnomAD v2.1

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 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.

Functional evidence
Statement recorded

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Loss-of-function; curated oncogenicity label: Likely Oncogenic.

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: 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.

Met Not met Not assessed Not applicable

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).

Met · 3

PS3 StrongIn 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. Details ▾Hide ▴
Rule
ENIGMA BRCA2 PS3 uses calibrated functional studies with code strength assigned in Table 9.
Evidence considered
  • Specifications Table 9 exact variant row: BRCA2 c.8168A>C p.(Asp2723Ala)
  • Pre-assigned code in Table 9: PS3 Strong
Sources
vcep_specifications_table9_v1_2_2024_11_18vcep_specifications_v1_2_2024_11_18
PP3 SupportingThis 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. Details ▾Hide ▴
Rule
ENIGMA BRCA2 PP3 applies to missense variants inside the defined functional domain with BayesDel >= 0.30, or to variants with predicted splice impact.
Evidence considered
  • Variant location p.Asp2723Ala within BRCA2 DNA binding domain aa 2481-3186
  • BayesDel 0.575545
  • REVEL 0.94
  • SpliceAI max delta 0.00
Sources
cspec ↗bayesdelrevelspliceai ↗vcep_specifications_v1_2_2024_11_18
PP5 SupportingExpert panel ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen classified as Pathogenic. Details ▾Hide ▴
Rule
Not applicable in ENIGMA BRCA2 specifications.
Evidence considered
  • PP5 listed as not applicable in the BRCA2 specification
  • ClinVar expert panel classification
Sources

Not met · 11 · evaluated, threshold not reached

PVS1 This missense variant does not fall into the BRCA2 loss-of-function categories used for PVS1, and SpliceAI predicts no significant splice effect (max delta score 0.00), so available evidence does not support a truncating or RNA loss-of-function mechanism for this change. Details ▾Hide ▴
Rule
ENIGMA BRCA2 PVS1 applies to null variants or qualifying RNA loss-of-function evidence.
Evidence considered
  • Missense change p.(Asp2723Ala)/p.(D2723A)
  • Generic PVS1 scaffold indicates this variant is outside default null-variant buckets
  • SpliceAI max delta score 0.00
Sources
cspec ↗pvs1_gene_contextpvs1_variant_assessmentspliceai ↗PMID:18451181 ↗
PS4 No case-control evidence showing a statistically increased prevalence of this variant in affected individuals versus controls was identified, and the reviewed ENIGMA posterior-probability and multifactorial resources did not provide an exact variant-specific PS4-qualifying result. Details ▾Hide ▴
Rule
ENIGMA BRCA2 PS4 requires significant enrichment in affected individuals compared with controls.
Evidence considered
  • No exact c.8168A>C / p.(Asp2723Ala) match retrieved from SupplementaryTables or HUMU lookup
  • PS4 requires case-control enrichment evidence
Sources
cspec ↗vcep_supplementarytables_v1_2_2024_11_18vcep_humu_40_1557_s001
PM2 ENIGMA PM2_Supporting requires absence from gnomAD, but this variant is present in gnomAD v2.1 at 1/251098 alleles (AF 3.98e-06) and in gnomAD v4.1 at 6/1614162 alleles (AF 3.72e-06), so PM2 is not met. Details ▾Hide ▴
Rule
ENIGMA BRCA2 PM2_Supporting requires absence from controls in gnomAD.
Evidence considered
  • gnomAD v2.1 total AC/AN 1/251098
  • gnomAD v4.1 total AC/AN 6/1614162
Sources
PP4 The BRCA2 clinical-history likelihood ratio for this variant is 1.329 with 2 probands, which falls in the ENIGMA neutral zone above 0.48 and below 2.08, so available clinical-history evidence does not support PP4. Details ▾Hide ▴
Rule
ENIGMA BRCA2 PP4 requires a clinical-history LR >= 2.08.
Evidence considered
  • Clinical-history LR 1.32919317721118
  • N_Probands 2
Sources
PMID:31853058 ↗vcep_pmid_31853058_brca2_clinical_history_lrvcep_pmid_31853058_li_2020_geneticsinmedicinecspec ↗
BA1 This variant is far below the BA1 threshold. In gnomAD v4.1 the highest available filter allele frequency is 1.83e-06, which is well below the ENIGMA BA1 cutoff of 0.001, so BA1 is not met. Details ▾Hide ▴
Rule
ENIGMA BRCA2 BA1 requires FAF > 0.1%.
Evidence considered
  • gnomAD v4.1 grpmax FAF 1.83e-06
  • BA1 threshold 0.001
Sources
BS1 This variant does not meet the BRCA2 BS1 frequency thresholds. The highest available filter allele frequency is 1.83e-06 in gnomAD v4.1, which is below the BS1_Supporting threshold of 0.00002 and below the BS1 threshold of 0.0001. Details ▾Hide ▴
Rule
ENIGMA BRCA2 BS1 uses FAF thresholds >0.00002 and >0.0001.
Evidence considered
  • gnomAD v4.1 grpmax FAF 1.83e-06
  • BS1_Supporting threshold 2e-05
  • BS1 threshold 1e-04
Sources
BS3 Available functional evidence does not support normal BRCA2 function. Instead, the curated ENIGMA functional dataset assigns PS3 Strong for this variant, so BS3 is not met. Details ▾Hide ▴
Rule
ENIGMA BRCA2 BS3 requires well-established studies showing no damaging effect.
Evidence considered
  • Table 9 exact variant row assigns PS3 Strong
  • not BS3
Sources
vcep_specifications_table9_v1_2_2024_11_18vcep_specifications_v1_2_2024_11_18
BP1 This missense variant is located within the BRCA2 DNA-binding functional region rather than outside a clinically important domain, so BP1 is not met. Details ▾Hide ▴
Rule
ENIGMA BRCA2 BP1 applies to missense or silent variants outside the defined functional domains with no predicted splice effect.
Evidence considered
  • Protein position 2723 lies within BRCA2 DNA binding region aa 2481-3186
Sources
cspec ↗vcep_specifications_v1_2_2024_11_18
BP4 Although SpliceAI predicts no significant splice impact (max delta score 0.00), the variant is in the BRCA2 DNA-binding region and the BayesDel score is 0.575545, which is above the BP4 benign threshold of 0.18. REVEL is also high at 0.94. Therefore, computational evidence does not support BP4. Details ▾Hide ▴
Rule
ENIGMA BRCA2 BP4 requires no predicted impact by protein change or splicing.
Evidence considered
  • BayesDel 0.575545
  • BP4 BayesDel threshold <=0.18
  • SpliceAI max delta 0.00
  • REVEL 0.94
Sources
cspec ↗bayesdelrevelspliceai ↗vcep_specifications_v1_2_2024_11_18
BP5 The BRCA2 clinical-history likelihood ratio for this variant is 1.329 with 2 probands, which is above the BP5 supporting cutoff of 0.48 and remains in the ENIGMA neutral zone, so BP5 is not met. Details ▾Hide ▴
Rule
ENIGMA BRCA2 BP5 requires a clinical-history LR <= 0.48.
Evidence considered
  • Clinical-history LR 1.32919317721118
  • N_Probands 2
Sources
PMID:31853058 ↗vcep_pmid_31853058_brca2_clinical_history_lrvcep_pmid_31853058_li_2020_geneticsinmedicinecspec ↗
BP7 This is a missense variant within the BRCA2 DNA-binding functional region, and available functional evidence supports a damaging protein effect rather than a benign RNA-only effect, so BP7 is not met. Details ▾Hide ▴
Rule
ENIGMA BRCA2 BP7 is used for qualifying silent, intronic, or RNA-only benign splicing evidence scenarios.
Evidence considered
  • Missense variant in BRCA2 DNA binding domain
  • Table 9 assigns PS3 Strong
  • SpliceAI max delta 0.00
Sources
cspec ↗vcep_specifications_table9_v1_2_2024_11_18spliceai ↗PMID:18451181 ↗

Not assessed · 5 · no assessment recorded

PS1 No qualifying reference variant with the same amino acid change and an established BRCA2 protein-based pathogenic classification was identified in the reviewed materials, so PS1 was not applied. Details ▾Hide ▴
Rule
ENIGMA BRCA2 PS1 requires the same amino acid substitution as an established pathogenic or likely pathogenic reference variant acting through protein change.
Evidence considered
  • PS1 requires a previously classified pathogenic or likely pathogenic variant causing the same amino acid change without a splice mechanism
Still missing
  • A curated same-amino-acid comparison set was not identified in the reviewed materials.
Sources
cspec ↗vcep_specifications_v1_2_2024_11_18clinvar ↗
PM3 No evidence was identified that this variant was observed in trans with another BRCA2 pathogenic variant in an individual with BRCA2-related Fanconi anemia, so PM3 could not be assessed. Details ▾Hide ▴
Rule
ENIGMA BRCA2 PM3 requires trans observations in BRCA2-related Fanconi anemia.
Evidence considered
  • PM3 in BRCA2 is restricted to Fanconi anemia-associated biallelic observations
Still missing
  • No Fanconi anemia phenotype and phase data were identified.
Sources
cspec ↗vcep_specifications_v1_2_2024_11_18
PP1 No quantitative co-segregation data were identified for this variant, so PP1 could not be applied. Details ▾Hide ▴
Rule
ENIGMA BRCA2 PP1 requires quantitative segregation evidence meeting LR thresholds.
Evidence considered
  • No exact variant-specific segregation result retrieved from reviewed multifactorial resources
Still missing
  • No segregation likelihood ratio was identified.
Sources
cspec ↗vcep_humu_40_1557_s001vcep_supplementarytables_v1_2_2024_11_18PMID:17924331 ↗PMID:16489001 ↗
BS2 No qualifying adult observations or point-based evidence against BRCA2-related Fanconi anemia were identified for this variant, so BS2 could not be assessed. Details ▾Hide ▴
Rule
ENIGMA BRCA2 BS2 requires point-based observations in the absence of Fanconi anemia features.
Evidence considered
  • BS2 in BRCA2 requires specific point-based observations
Still missing
  • No BS2 point-based clinical observations were identified.
Sources
cspec ↗vcep_specifications_v1_2_2024_11_18
BS4 No quantitative lack-of-segregation evidence was identified for this variant, so BS4 could not be applied. Details ▾Hide ▴
Rule
ENIGMA BRCA2 BS4 requires quantitative non-segregation evidence meeting LR thresholds.
Evidence considered
  • No exact variant-specific BS4 result retrieved from reviewed multifactorial resources
Still missing
  • No non-segregation likelihood ratio was identified.
Sources
cspec ↗vcep_humu_40_1557_s001vcep_supplementarytables_v1_2_2024_11_18PMID:17924331 ↗PMID:16489001 ↗
Not applicable · 9· recorded as not applicable Show reasons ▾Hide reasons ▴
PS2 N/AThis VCEP framework does not use PS2 for BRCA2. Details ▾Hide ▴
Rule
Not applicable in ENIGMA BRCA2 specifications.
Evidence considered
  • PS2 listed as not applicable in the BRCA2 specification
Sources
PM1 N/APM1 is not used as a standalone criterion in the BRCA2 specification because domain information is incorporated into the bioinformatic framework for PP3, BP4, and BP1. Details ▾Hide ▴
Rule
Not applicable as a standalone criterion in ENIGMA BRCA2.
Evidence considered
  • PM1 marked not applicable in BRCA2 specification
Sources
cspec ↗vcep_specifications_v1_2_2024_11_18
PM4 N/APM4 is not used in this BRCA2 specification. Details ▾Hide ▴
Rule
Not applicable in ENIGMA BRCA2 specifications.
Evidence considered
  • PM4 listed as not applicable in the BRCA2 specification
Sources
PM5 N/AIn this BRCA2 framework, PM5 is used for protein-termination variants in eligible exons, not for this missense substitution. Details ▾Hide ▴
Rule
ENIGMA BRCA2 PM5 is configured as PM5_PTC for qualifying truncating variants.
Evidence considered
  • Variant is missense
  • not a protein-termination variant
Sources
cspec ↗vcep_specifications_table4_v1_2_2024_11_18
PM6 N/AThis VCEP framework does not use PM6 for BRCA2. Details ▾Hide ▴
Rule
Not applicable in ENIGMA BRCA2 specifications.
Evidence considered
  • PM6 listed as not applicable in the BRCA2 specification
Sources
PP2 N/AThis VCEP framework does not use PP2 for BRCA2. Details ▾Hide ▴
Rule
Not applicable in ENIGMA BRCA2 specifications.
Evidence considered
  • PP2 listed as not applicable in the BRCA2 specification
Sources
BP2 N/AThis VCEP framework does not use BP2 for BRCA2. Details ▾Hide ▴
Rule
Not applicable in ENIGMA BRCA2 specifications.
Evidence considered
  • BP2 listed as not applicable in the BRCA2 specification
Sources
BP3 N/ABP3 is not used in this BRCA2 specification. Details ▾Hide ▴
Rule
Not applicable in ENIGMA BRCA2 specifications.
Evidence considered
  • BP3 listed as not applicable in the BRCA2 specification
Sources
BP6 N/AThis VCEP framework does not use BP6 for BRCA2. Details ▾Hide ▴
Rule
Not applicable in ENIGMA BRCA2 specifications.
Evidence considered
  • BP6 listed as not applicable in the BRCA2 specification
Sources

Identifiers

Gene
BRCA2
Transcript
NM_000059.3
Coding (HGVS c.)
NM_000059.3:c.8168A>C
Protein (HGVS p.)
NP_000050.2:p.(Asp2723Ala)
GRCh38
chr13:32363370 A>C
GRCh37
chr13:32937507 A>C

Gene diagram

Every interpreted variant in BRCA2, mapped onto the exon structure of NM_000059.3. Select a row to find it on the plot.

BRCA2NM_000059.3
Fetching transcript structure from UCSC…
gnomAD v4.1 6 / 1,614,162 alleles AF 3.72e-06 · 0 homozygotes · FAF 1.83e-06
gnomAD v2.1 1 / 251,098 alleles AF 3.98e-06 · 0 homozygotes

By genetic ancestry

gnomAD v4.1

AF 3.7e-06 · 6 / 1,614,162 alleles · 0 hom · FAF 1.8e-06
European (non-Finnish)6 / 1,180,024 5.1e-06
0 alternate alleles recorded in 9 other groups: Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American.

gnomAD v2.1

AF 4e-06 · 1 / 251,098 alleles · 0 hom
European (non-Finnish)1 / 113,396 8.8e-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= 3.7171e-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.

gnomAD v2.1

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).

Other predictors

REVEL
Not available
BayesDel
Not available

How the predictions were used

PP3 SupportingThis 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. Details ▾Hide ▴
Rule
ENIGMA BRCA2 PP3 applies to missense variants inside the defined functional domain with BayesDel >= 0.30, or to variants with predicted splice impact.
Evidence considered
  • Variant location p.Asp2723Ala within BRCA2 DNA binding domain aa 2481-3186
  • BayesDel 0.575545
  • REVEL 0.94
  • SpliceAI max delta 0.00
Sources
cspec ↗bayesdelrevelspliceai ↗vcep_specifications_v1_2_2024_11_18
BP4 Although SpliceAI predicts no significant splice impact (max delta score 0.00), the variant is in the BRCA2 DNA-binding region and the BayesDel score is 0.575545, which is above the BP4 benign threshold of 0.18. REVEL is also high at 0.94. Therefore, computational evidence does not support BP4. Details ▾Hide ▴
Rule
ENIGMA BRCA2 BP4 requires no predicted impact by protein change or splicing.
Evidence considered
  • BayesDel 0.575545
  • BP4 BayesDel threshold <=0.18
  • SpliceAI max delta 0.00
  • REVEL 0.94
Sources
cspec ↗bayesdelrevelspliceai ↗vcep_specifications_v1_2_2024_11_18
BP7 This is a missense variant within the BRCA2 DNA-binding functional region, and available functional evidence supports a damaging protein effect rather than a benign RNA-only effect, so BP7 is not met. Details ▾Hide ▴
Rule
ENIGMA BRCA2 BP7 is used for qualifying silent, intronic, or RNA-only benign splicing evidence scenarios.
Evidence considered
  • Missense variant in BRCA2 DNA binding domain
  • Table 9 assigns PS3 Strong
  • SpliceAI max delta 0.00
Sources
cspec ↗vcep_specifications_table9_v1_2_2024_11_18spliceai ↗PMID:18451181 ↗

Statement

In silico

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.

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= 3.7171e-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.

gnomAD v2.1

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).

ClinVar

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).

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.94. BayesDel score = 0.575545.

Functional

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Loss-of-function; curated oncogenicity label: Likely Oncogenic.

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.