About BRCA2
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
BRCA2 c.3069_3074del, p.(Asn1023_Ile1024del)
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.
Words with a dotted underline have a short definition. Hover or tap them.
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: 1
Pathogenic criteria applied · 0
No pathogenic criterion marked as applied in the recorded assessment.
Benign criteria applied · 1
BP1Strong
BP1 · strong
ENIGMA BP1_Strong applies to in-frame deletions outside a clinically important functional domain with no splicing predicted (SpliceAI ≤0.1). This variant is an in-frame deletion removing amino acids 1023-1024, which lies outside both ENIGMA-defined clinically important functional domains for BRCA2 (PALB2 binding domain aa 10-40; DNA binding domain aa 2481-3186). SpliceAI max delta score = 0.00, confirming no predicted splicing impact. Both conditions for BP1_Strong are satisfied.
Recorded classification: Likely benign
ENIGMA BRCA1/BRCA2 Table 3 framework (v1.2.0) applied. The sole met criterion is BP1_Strong: the variant is an in-frame deletion of two amino acids (p.Asn1023_Ile1024del) located outside the ENIGMA-defined clinically important functional domains (PALB2 binding domain aa 10-40; DNA binding domain aa 2481-3186), and SpliceAI max delta = 0.00 confirms no splicing impact. Under ENIGMA Table 3, a single Strong (Benign) criterion qualifies as Likely Benign when supported by multiple independent evidence types — satisfied here because BP1_Strong itself draws on two distinct evidence modalities: protein domain architecture and computational splicing prediction. No pathogenic criteria are met, so no conflicting-evidence point calculation is needed.
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
7 / 1,613,238 alleles
gnomAD v4.1: 7 / 1,613,238 alleles. Recorded AF 4.3391e-06. Recorded homozygote count 0.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 7.10172e-06; MAF= 0.00071%, 2/281622 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 8.06907e-05; MAF= 0.00807%, 2/24786 alleles, homozygotes = 0).
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
No listed criterion applied
SpliceAI score
0.000 maximum delta
Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.
No listed criterion applied
SpliceAI ↗
ClinVar submissions
3 reported laboratory submissions
3 Uncertain significance.
Context only
ClinVar ↗
Functional evidence
Statement recorded
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. 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
No matching record reported
This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.
Context only
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: 1 met · 14 not met · 0 not assessed · 13 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
NM_000059.3:c.3069_3074del (p.Asn1023_Ile1024del) is an in-frame deletion of 6 bp in BRCA2 exon 11, removing two amino acids outside the ENIGMA-defined clinically important functional domains.
BP1_Strong is applied: the variant is an in-frame deletion located outside the PALB2 binding domain (aa 10-40) and DNA binding domain (aa 2481-3186), and SpliceAI predicts no splicing impact (delta = 0.00).
No other pathogenic or benign criteria are met. PVS1 is not applicable to this in-frame intra-exonic deletion under ENIGMA Table 4. PM2 is not met as the variant is present in gnomAD population controls (v2.1: 2/281,622 alleles; v4.1: 7/1,613,238). PP3 is not met as the variant is outside functional domains and SpliceAI shows no splicing impact. PP4 and BP5 are not met as the variant is absent from the Li et al. 2020 clinical-history LR table. BA1 and BS1 are not met as gnomAD FAF (1.75e-05) is below both thresholds.
With a single BP1_Strong criterion and no other criteria met in either direction, the variant does not reach the ENIGMA Likely Benign threshold (requires Strong + Supporting benign, Strong + Moderate benign, or Moderate + Supporting benign). The variant is classified as a Variant of Uncertain Significance.
No criteria match.
Met · 1
BP1 StrongENIGMA BP1_Strong applies to in-frame deletions outside a clinically important functional domain with no splicing predicted (SpliceAI ≤0.1). This variant is an in-frame deletion removing amino acids 1023-1024, which lies outside both ENIGMA-defined clinically important functional domains for BRCA2 (PALB2 binding domain aa 10-40; DNA binding domain aa 2481-3186). SpliceAI max delta score = 0.00, confirming no predicted splicing impact. Both conditions for BP1_Strong are satisfied. Details ▾Hide ▴
Evidence considered
- In-frame deletion at aa 1023-1024
- outside functional domains (aa 10-40
- 2481-3186). SpliceAI delta = 0.00 (≤0.1). Meets ENIGMA BP1_Strong criteria.
Sources
Not met · 14 · evaluated, threshold not reached
PVS1 NM_000059.3:c.3069_3074del is an in-frame deletion of 6 bp in BRCA2 exon 11, resulting in deletion of two amino acids (p.Asn1023_Ile1024del). ENIGMA PVS1 criteria are restricted to null variants (nonsense, frameshift, canonical ±1,2 splice site, initiation codon, or whole-exon deletion). This in-frame intra-exonic deletion does not qualify as a null variant under ENIGMA Table 4 specifications. No downgrade or alternative PVS1 strength applies. Details ▾Hide ▴
Evidence considered
- In-frame deletion of 2 amino acids in exon 11
- not a null variant per ENIGMA Table 4. PVS1 not assigned to in-frame intra-exonic deletions in BRCA2 exon 11.
Sources
vcep_specifications_table4_v1_2_2024_11_18
PS3 Variant is not listed in ENIGMA Specifications Table 9 (calibrated functional assay results for BRCA2). No variant-specific functional data from calibrated mammalian studies meeting ENIGMA PS3 thresholds were identified. Shi et al. (2025, PMID:40664060) performed in silico splicing analysis only for this variant (no splicing impact) and did not conduct variant-specific wet-lab functional assays; their functional validation was limited to the BRCA2 p.W2619C variant. Details ▾Hide ▴
Evidence considered
- Not present in ENIGMA Table 9. Shi et al. 2025 performed only in silico splicing analysis (no impact) for this variant
- no variant-specific calibrated functional data.
Still missing
- No variant-specific functional assay data available.
Sources
vcep_specifications_table9_v1_2_2024_11_18PMID:40664060 ↗
PS4 ENIGMA PS4 requires a case-control study demonstrating significantly increased prevalence in affected individuals versus controls (p≤0.05 and OR≥4, lower CI excludes 2.0). No such case-control study was identified for this variant. The variant has been observed in gnomAD population controls (2/281,622 alleles in v2.1; 7/1,613,238 in v4.1) and in one breast cancer patient in Shi et al. (2025), but no formal case-control comparison meeting ENIGMA thresholds is available. Details ▾Hide ▴
Evidence considered
- Present at very low frequency in population controls. One proband reported in Shi et al. 2025. No case-control study with OR≥4 identified.
Still missing
- No case-control data meeting ENIGMA PS4 thresholds.
Sources
PM2 ENIGMA PM2_Supporting requires absence from gnomAD v2.1 (non-cancer, exome only subset) and gnomAD v3.1 (non-cancer) in an outbred population. This variant is present in gnomAD v2.1 (2/281,622 alleles, AF=7.1e-06) and gnomAD v4.1 (7/1,613,238 alleles, AF=4.3e-06). The variant is not absent from population controls. Details ▾Hide ▴
Evidence considered
- Present in gnomAD v2.1 (2/281
- 622 alleles) and v4.1 (7/1
- 613
- 238). Does not meet ENIGMA PM2 absence requirement.
Sources
PP1 ENIGMA PP1 requires quantitative co-segregation analysis with likelihood ratio ≥2.08:1 (Supporting), ≥4.3:1 (Moderate), or ≥18.7:1 (Strong). No co-segregation data are available for this variant. Details ▾Hide ▴
Evidence considered
- No co-segregation data available.
Still missing
- No segregation analysis data.
PP3 ENIGMA PP3 applies to: (a) in-frame deletions inside a clinically important functional domain with BayesDel ≥0.30, or (b) variants with SpliceAI ≥0.2 irrespective of location. This variant at amino acids 1023-1024 is outside the ENIGMA-defined clinically important functional domains (PALB2 binding domain aa 10-40; DNA binding domain aa 2481-3186). SpliceAI max delta = 0.00, well below the 0.2 threshold. Neither condition is met. Details ▾Hide ▴
Evidence considered
- Outside functional domains (aa 10-40
- 2481-3186)
- variant at aa 1023-1024. SpliceAI delta = 0.00. No BayesDel score available (not SNV).
Sources
PP4 ENIGMA PP4 requires clinical-history likelihood ratio ≥2.08:1 from the Li et al. 2020 (PMID:31853058) BRCA2 clinical-history LR table. The variant NM_000059.3:c.3069_3074del is not listed in this table. A related variant c.3069delC is present (LR=0.79, neutral zone) but this is a different variant and does not provide evidence for c.3069_3074del. Details ▾Hide ▴
Evidence considered
- Variant not present in Li et al. 2020 BRCA2 clinical-history LR table. Nearby variant c.3069delC has LR=0.79 (neutral
- not applicable by identity).
Still missing
- No clinical-history LR data for this exact variant.
Sources
vcep_pmid_31853058_brca2_clinical_history_lrPMID:31853058 ↗
BA1 ENIGMA BA1 requires filter allele frequency (FAF) above 0.1% (0.001) in gnomAD. gnomAD v4.1 joint grpmax FAF = 1.746e-05 (0.001746%), far below the 0.1% threshold. Details ▾Hide ▴
Evidence considered
- gnomAD v4.1 FAF = 1.746e-05 (0.00175%)
- below BA1 threshold of 0.1%.
Sources
BS1 ENIGMA BS1_Supporting requires FAF >0.002% (0.00002) and BS1_Strong requires FAF >0.01% (0.0001). gnomAD v4.1 joint grpmax FAF = 1.746e-05 (0.001746%), which is below the BS1_Supporting threshold of 0.002%. Neither BS1 strength level is met. Details ▾Hide ▴
Evidence considered
- gnomAD v4.1 FAF = 1.746e-05 (0.00175%)
- below BS1_Supporting threshold of 0.002%.
Sources
BS2 ENIGMA BS2 requires observation in healthy adults without Fanconi Anemia phenotype, using a points-based system (Specifications Table 8). No such data have been reported for this variant. Details ▾Hide ▴
Evidence considered
- No observations in healthy adults without Fanconi Anemia reported.
Still missing
- No BS2 qualifying observations available.
BS3 Variant is not listed in ENIGMA Specifications Table 9 (calibrated functional assay results for BRCA2). No variant-specific functional data demonstrating no damaging effect are available. Details ▾Hide ▴
Evidence considered
- Not present in ENIGMA Table 9. No calibrated functional data showing no damaging effect.
Still missing
- No variant-specific functional data.
Sources
vcep_specifications_table9_v1_2_2024_11_18
BS4 ENIGMA BS4 requires lack of segregation in affected family members with likelihood ratio ≤0.48:1 (Supporting), ≤0.23:1 (Moderate), or ≤0.05:1 (Strong). No segregation data are available for this variant. Details ▾Hide ▴
Evidence considered
- No segregation data available.
Still missing
- No segregation analysis data.
BP4 ENIGMA BP4 applies to in-frame deletions inside a clinically important functional domain with BayesDel ≤0.18 and SpliceAI ≤0.1. This variant at amino acids 1023-1024 is outside the ENIGMA-defined clinically important functional domains (aa 10-40 and aa 2481-3186). BP4 domain requirement is not satisfied. Details ▾Hide ▴
Evidence considered
- Variant at aa 1023-1024 is outside functional domains
- BP4 requires variants inside a functional domain.
Sources
BP5 ENIGMA BP5 requires clinical-history likelihood ratio ≤0.48:1 from the Li et al. 2020 (PMID:31853058) BRCA2 clinical-history LR table. The variant is not listed in this table. No multifactorial likelihood data supporting benignity are available. Details ▾Hide ▴
Evidence considered
- Variant not present in Li et al. 2020 clinical-history LR table. No LR data available.
Still missing
- No clinical-history LR data for this variant.
Sources
vcep_pmid_31853058_brca2_clinical_history_lr
Not applicable · 13· recorded as not applicable Show reasons ▾Hide reasons ▴
PS1 N/AENIGMA PS1 applies only to missense substitutions sharing the same residue as a previously classified pathogenic missense variant, or to exonic/intronic variants with the same predicted splicing impact as a previously classified pathogenic variant. This is an in-frame deletion, not a missense substitution or splicing variant. Details ▾Hide ▴
Evidence considered
- In-frame deletion
- does not meet ENIGMA PS1 applicability criteria.
PS2 VCEPENIGMA specification marks PS2 as Not Applicable. Details ▾Hide ▴
No further detail was recorded.
PM1 VCEPENIGMA specification marks PM1 as Not Applicable. Details ▾Hide ▴
No further detail was recorded.
PM4 VCEPENIGMA specification marks PM4 as Not Applicable. Details ▾Hide ▴
No further detail was recorded.
PM5 N/AENIGMA PM5 is repurposed for protein termination codon (PTC) variants only, applied as additional weight for PTC variants already annotated as PVS1. This is an in-frame deletion (p.Asn1023_Ile1024del), not a PTC variant. PM5 classic same-residue missense logic also does not apply (not a missense substitution). Details ▾Hide ▴
Evidence considered
- In-frame deletion
- not a PTC variant. ENIGMA PM5 restricted to PTC variants.
Sources
vcep_specifications_table4_v1_2_2024_11_18
PM6 VCEPENIGMA specification marks PM6 as Not Applicable. Details ▾Hide ▴
No further detail was recorded.
PP2 VCEPENIGMA specification marks PP2 as Not Applicable. Details ▾Hide ▴
No further detail was recorded.
PP5 VCEPENIGMA specification marks PP5 as Not Applicable. Details ▾Hide ▴
No further detail was recorded.
BP2 VCEPENIGMA specification marks BP2 as Not Applicable. Details ▾Hide ▴
No further detail was recorded.
BP3 VCEPENIGMA specification marks BP3 as Not Applicable. Details ▾Hide ▴
No further detail was recorded.
BP6 VCEPENIGMA specification marks BP6 as Not Applicable. Details ▾Hide ▴
No further detail was recorded.
BP7 N/AENIGMA BP7 applies to silent variants inside clinically important functional domains (if BP4 met), intronic variants outside conserved splice motifs (if BP4 met), or variants with RNA assay evidence showing no damaging effect on mRNA transcript profile. This is an in-frame deletion; none of these conditions apply. Details ▾Hide ▴
Evidence considered
- In-frame deletion
- does not meet ENIGMA BP7 applicability (silent/intronic/RNA assay variants only).
PS5 N/AENIGMA specification marks PP5 as Not Applicable; PS5 follows the same logic as the generic ACMG/AMP counterpart to PP5. Details ▾Hide ▴
No further detail was recorded.
Identifiers
- Gene
- BRCA2
- Transcript
- NM_000059.3
- Coding (HGVS c.)
- NM_000059.3:c.3069_3074del
- Protein (HGVS p.)
- NP_000050.2:p.(Asn1023_Ile1024del)
- GRCh38
- chr13:32337420 ATAACAT>A
- GRCh37
- chr13:32911557 ATAACAT>A
- ClinVar
- 182312
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…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in BRCA2
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Select a row to find it on the plot; use the link to open its page.
| Protein | Location | Classification | Link |
|---|
gnomAD v4.1
7 / 1,613,238 alleles
AF 4.34e-06 · 0 homozygotes · FAF 1.75e-05
gnomAD v2.1
2 / 281,622 alleles
AF 7.1e-06 · 0 homozygotes
gnomAD-Canada v1.0
Allele count data not recorded
By genetic ancestry
gnomAD v4.1
AF 4.3e-06 · 7 / 1,613,238 alleles · 0 hom · FAF 1.7e-05
| African/African American4 / 74,918 | 5.3e-05 |
| European (non-Finnish)3 / 1,179,562 | 2.5e-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 7.1e-06 · 2 / 281,622 alleles · 0 hom
| African/African American2 / 24,786 | 8.1e-05 |
0 alternate alleles recorded in 7 other groups: Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian.
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 4.3391e-06; MAF= 0.00043%, 7/1613238 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 5.33917e-05; MAF= 0.00534%, 4/74918 alleles, homozygotes = 0); grpmax FAF= 1.746e-05.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 7.10172e-06; MAF= 0.00071%, 2/281622 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 8.06907e-05; MAF= 0.00807%, 2/24786 alleles, homozygotes = 0).
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI and Pangolin
Other predictors
- REVEL
- Not available
- BayesDel
- Not available
How the predictions were used
PP3 ENIGMA PP3 applies to: (a) in-frame deletions inside a clinically important functional domain with BayesDel ≥0.30, or (b) variants with SpliceAI ≥0.2 irrespective of location. This variant at amino acids 1023-1024 is outside the ENIGMA-defined clinically important functional domains (PALB2 binding domain aa 10-40; DNA binding domain aa 2481-3186). SpliceAI max delta = 0.00, well below the 0.2 threshold. Neither condition is met. Details ▾Hide ▴
Evidence considered
- Outside functional domains (aa 10-40
- 2481-3186)
- variant at aa 1023-1024. SpliceAI delta = 0.00. No BayesDel score available (not SNV).
Sources
BP4 ENIGMA BP4 applies to in-frame deletions inside a clinically important functional domain with BayesDel ≤0.18 and SpliceAI ≤0.1. This variant at amino acids 1023-1024 is outside the ENIGMA-defined clinically important functional domains (aa 10-40 and aa 2481-3186). BP4 domain requirement is not satisfied. Details ▾Hide ▴
Evidence considered
- Variant at aa 1023-1024 is outside functional domains
- BP4 requires variants inside a functional domain.
Sources
BP7 N/AENIGMA BP7 applies to silent variants inside clinically important functional domains (if BP4 met), intronic variants outside conserved splice motifs (if BP4 met), or variants with RNA assay evidence showing no damaging effect on mRNA transcript profile. This is an in-frame deletion; none of these conditions apply. Details ▾Hide ▴
Evidence considered
- In-frame deletion
- does not meet ENIGMA BP7 applicability (silent/intronic/RNA assay variants only).
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
7 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata.
Recorded publications
-
PMID 23918944 ↗Tamoxifen and risk of contralateral breast cancer for BRCA1 and BRCA2 mutation carriers.Phillips et al. (2013) examined tamoxifen and contralateral breast cancer risk in BRCA1 and BRCA2 mutation carriers using pooled observational cohort data. NM_000059.3:c.3069_3074del was not identified in this paper.Does not name this variant
-
PMID 40664060 ↗Characterization and functional analysis of BRCA1 and BRCA2 variants in a cohort of 100 unselected patients undergoing germline screening.Shi Q et al. · 2025Shi et al. (2025) identified BRCA2 c.3069_3074del (p.N1023_I1024del) in one breast cancer patient from a cohort of 100 unselected patients undergoing germline screening. The variant was classified as VUS using generic ACMG/AMP criteria (PM4, PM2_Supporting). SpliceAI analysis showed no splicing impact. Study authors constructed an expression plasmid for this variant but functional assays (western blot, migration, invasion, PARP inhibitor sensitivity) were performed only for BRCA2 p.W2619C; no variant-specific wet-lab functional data were generated for p.N1023_I1024del.Names this variant
Quoted passage
functional impairment confirmed for the BRCA2 p.W2619C and BRCA2 p.N1023_I1024del variants
Abstract; Table 2 (Sample 3); Table 4; Results section 'Evaluation of nine VUS mutations'; Materials and Methods 'Construction of expression plasmids'
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PMID 17392385 ↗American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography.Saslow D et al. · 2007Saslow et al. (2007) published American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography. This is a clinical practice guideline and does not mention specific BRCA2 variants.Does not name this variant
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PMID 23788249 ↗ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing.Green et al. (2013) published ACMG recommendations for reporting incidental findings in clinical exome and genome sequencing. This is a policy statement and does not mention specific BRCA2 variants.Does not name this variant
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PMID 24493721 ↗American Society of Clinical Oncology Expert Statement: collection and use of a cancer family history for oncology providers.Luu et al. (2014) published an ASCO expert statement on collection and use of cancer family history. This is a clinical guidance document and does not mention specific BRCA2 variants.Does not name this variant
-
PMID 27854360 ↗Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics.Kalia et al. (2017) published the 2016 ACMG update on reporting secondary findings in clinical exome and genome sequencing. This is a policy statement and does not mention specific BRCA2 variants.Does not name this variant
-
PMID 30287823 ↗Germline pathogenic variants of 11 breast cancer genes in 7,051 Japanese patients and 11,241 controls.Momozawa Y et al. · 2018Momozawa et al. (2018) performed a case-control association study of 11 breast cancer genes in 7,051 Japanese patients and 11,241 controls. NM_000059.3:c.3069_3074del was not identified in this paper.Does not name this variant
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
7 / 1,613,238 recorded alleles
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.000
Open source ↗
ClinVar
3 Uncertain significance
Open source ↗
COSMIC
Captured COSMIC source record
Open source ↗
Cancer hotspots
Captured Cancer Hotspots source record
Open source ↗
OncoKB
Captured OncoKB source record
Open source ↗
ClinGen CSpec
Captured ClinGen CSpec source record
Open source ↗
All source links
- ClinGen CSpec ↗cspec.genome.network/cspec/ui/svi/doc/1535438831
- ClinVar ↗www.ncbi.nlm.nih.gov/clinvar/variation/182312/
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/13-32911557-ATAACAT-A?dataset…
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr13-32337420-ATAACAT-A?data…
- gnomAD-Canada ↗http://192.168.4.76:8001/variant/13-32337420-ATAACAT-A
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_000059.3%3Ac.3069…
- OncoKB ↗www.oncokb.org/gene/BRCA2/N1023_I1024del
- COSMIC ↗cancer.sanger.ac.uk/cosmic/search?q=BRCA2+c.3069_3074del
- Cancer hotspots ↗www.cancerhotspots.org/
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= 4.3391e-06; MAF= 0.00043%, 7/1613238 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 5.33917e-05; MAF= 0.00534%, 4/74918 alleles, homozygotes = 0); grpmax FAF= 1.746e-05.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 7.10172e-06; MAF= 0.00071%, 2/281622 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 8.06907e-05; MAF= 0.00807%, 2/24786 alleles, homozygotes = 0).
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
ClinVar
This variant has been reported in ClinVar as Uncertain significance (3 clinical laboratories). (ClinVarID = 182312)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
Functional
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. 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.