BRCA2c.1909+11_1909+12delLikely benign

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Variant interpretation report

BRCA2 c.1909+11_1909+12del, p.?

NM_000059.4:c.1909+11_1909+12del NP_000050.3:p.? 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.

Key facts

Evidence used: 2 supporting (benign)
Expert rules: ClinGen BRCA2 VCEP v1.2.0
Pipeline record: 10 Jun 2026

Evidence considered

View criteria

Applied evidence criteria

BP4 (supporting): NM_000059.4:c.1909+11_1909+12del is an intronic deletion at positions +11 and +12 of intron 10, outside the native donor splice consensus (+/-1,2). SpliceAI predicts no splicing impact (max delta = 0.00, ≤0.1). BP4_Supporting is met per ENIGMA BRCA2 specification Figure 1A.
BP7 (supporting): The intronic deletion is located at position +11, outside the conserved donor motif (beyond +7). BP4 is met (SpliceAI max delta = 0.00 ≤ 0.1). BP7_Supporting is met per ENIGMA BRCA2 specification Figure 1A and Appendix J.

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

BP4Supporting

BP4 · supporting

NM_000059.4:c.1909+11_1909+12del is an intronic deletion at positions +11 and +12 of intron 10, outside the native donor splice consensus (+/-1,2). SpliceAI predicts no splicing impact (max delta = 0.00, ≤0.1). BP4_Supporting is met per ENIGMA BRCA2 specification Figure 1A.

BP7Supporting

BP7 · supporting

The intronic deletion is located at position +11, outside the conserved donor motif (beyond +7). BP4 is met (SpliceAI max delta = 0.00 ≤ 0.1). BP7_Supporting is met per ENIGMA BRCA2 specification Figure 1A and Appendix J.

Recorded classification: Likely benign

ENIGMA BRCA1/BRCA2 Specification v1.2 Table 3: two Supporting (Benign) criteria (BP4_Supporting, BP7_Supporting) met, zero pathogenic criteria met. Matches the likely_benign rule requiring >=2 Supporting (Benign) criteria.

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

Not recorded

gnomAD v4.1 allele counts were not recorded for this variant.

gnomAD v2.1

Absent from gnomAD v2.1.

No listed criterion applied

gnomAD v4.1 ↗gnomAD v2.1 ↗gnomAD-Canada ↗

SpliceAI score

0.000 maximum delta

Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.

Applied · BP4, BP7 → SpliceAI ↗

ClinVar submissions

Not recorded

A ClinVar laboratory submission summary was not recorded.

Context only ClinVar ↗

No screenshot for this evidence

Functional evidence

Not recorded

No standalone functional evidence summary is recorded in evidence_summary.functional.

No listed criterion applied OncoKB ↗

Somatic evidence

No matching record reported

This variant has not previously been reported in somatic cancers (COSMIC).

Context only COSMIC ↗

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 · 5 not met · 8 not assessed · 13 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Pathogenic

PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 PS5

Benign

BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7

Met Not met Not assessed Not applicable

NM_000059.4:c.1909+11_1909+12del is an intronic deletion at positions +11 and +12 of intron 10, outside the native donor splice consensus (+/-1,2). SpliceAI predicts no splicing impact (max delta = 0.00). BP4_Supporting is met per ENIGMA BRCA2 specification Figure 1A.

The variant is located at intronic position +11, outside the conserved donor motif (beyond +7). BP4 is met (SpliceAI ≤0.1). BP7_Supporting is met per ENIGMA BRCA2 specification Figure 1A and Appendix J.

No pathogenic criteria are met. PVS1 is not met (outside canonical +/-1,2 splice consensus; does not qualify as a null variant per ENIGMA PVS1 criteria). PM2 is explicitly not applicable for deletion variants per ENIGMA specification. PP3 is not met (SpliceAI max delta = 0.00 < 0.2). Two supporting benign criteria are met (BP4_Supporting, BP7_Supporting). Per ENIGMA Table 3 combining rules, ≥2 Supporting (Benign) criteria supports classification as Likely Benign.

Met · 2

BP4 SupportingNM_000059.4:c.1909+11_1909+12del is an intronic deletion at positions +11 and +12 of intron 10, outside the native donor splice consensus (+/-1,2). SpliceAI predicts no splicing impact (max delta = 0.00, ≤0.1). BP4_Supporting is met per ENIGMA BRCA2 specification Figure 1A. Details ▾Hide ▴

Evidence considered

SpliceAI max delta = 0.00 ≤ 0.1
Intronic deletion at +11/+12
outside canonical +/-1
2 donor splice sites

Sources

spliceai ↗cspec ↗

BP7 SupportingThe intronic deletion is located at position +11, outside the conserved donor motif (beyond +7). BP4 is met (SpliceAI max delta = 0.00 ≤ 0.1). BP7_Supporting is met per ENIGMA BRCA2 specification Figure 1A and Appendix J. Details ▾Hide ▴

Evidence considered

Intronic variant at +11 position
outside conserved donor motif (beyond +7)
BP4 met (SpliceAI max delta = 0.00 ≤ 0.1)

Sources

spliceai ↗cspec ↗

Not met · 5 · evaluated, threshold not reached

PVS1 NM_000059.4:c.1909+11_1909+12del is an intronic deletion at positions +11 and +12 of intron 10, outside the canonical donor splice consensus (+/-1,2). Does not meet ENIGMA PVS1 null-variant criteria (nonsense, frameshift, canonical +/-1,2 splice, initiation codon, or exon-level deletion). Details ▾Hide ▴

Evidence considered

Intronic deletion at +11/+12
outside canonical +/-1
2 splice consensus

Sources

cspec ↗

PS1 SpliceAI predicts no splicing impact (max delta = 0.00). No previously classified pathogenic variant with the same predicted splicing effect available as comparator. PS1 is not met. Details ▾Hide ▴

Evidence considered

SpliceAI max delta = 0.00
no splicing impact predicted

Sources

spliceai ↗cspec ↗

PP3 SpliceAI predicts no significant splice impact (max delta = 0.00), well below the ENIGMA PP3 threshold of SpliceAI ≥0.2 for intronic variants outside donor/acceptor +/-1,2 sites. Details ▾Hide ▴

Evidence considered

SpliceAI max delta = 0.00
below ENIGMA PP3 threshold of ≥0.2

Sources

spliceai ↗cspec ↗

BA1 Variant is absent from gnomAD v2.1 and v4.1. BA1 threshold (FAF > 0.1% in non-founder populations) is not met. Details ▾Hide ▴

Evidence considered

Absent from gnomAD v2.1 and v4.1

Sources

gnomad_v2 ↗gnomad_v4 ↗cspec ↗

BS1 Variant is absent from gnomAD v2.1 and v4.1. Does not meet ENIGMA BS1 thresholds (FAF > 0.00002 for Supporting; FAF > 0.0001 for Strong). Details ▾Hide ▴

Evidence considered

Absent from gnomAD v2.1 and v4.1

Sources

gnomad_v2 ↗gnomad_v4 ↗cspec ↗

Not assessed · 8 · no assessment recorded

PS3 No functional assay data available for this intronic deletion variant in ENIGMA Specifications Table 9 or published literature. Details ▾Hide ▴

Still missing

No functional assay data for this intronic deletion

PS4 Variant is absent from ClinVar and COSMIC. No case-control study data available for prevalence comparison per ENIGMA PS4 specification. Details ▾Hide ▴

Evidence considered

Absent from ClinVar
no case-control data

Still missing

No case-control study data available

Sources

clinvar ↗

PP1 No co-segregation data available for quantitative analysis per ENIGMA PP1 specification. Details ▾Hide ▴

Still missing

No co-segregation data available

PP4 Variant is not listed in the Li et al. 2020 (PMID:31853058) BRCA2 clinical-history likelihood-ratio table. No clinical-history LR data available for PP4 assessment. Details ▾Hide ▴

Evidence considered

Variant absent from Li et al. 2020 BRCA2 clinical_history_LR table

Still missing

No clinical-history LR data for this variant

Sources

PMID:31853058 ↗31853058

BS2 No proband-level data available to evaluate for BS2 points under ENIGMA Specifications Table 8 (absence of Fanconi Anemia phenotype). Details ▾Hide ▴

Still missing

No proband phenotype data available

BS3 No functional assay data available for this intronic deletion variant in ENIGMA Specifications Table 9 or published literature. Details ▾Hide ▴

Still missing

No functional assay data for this intronic deletion

BS4 No segregation data available for quantitative BS4 likelihood-ratio analysis per ENIGMA specification. Details ▾Hide ▴

Still missing

No segregation data available

BP5 Variant is not listed in the Li et al. 2020 (PMID:31853058) BRCA2 clinical-history likelihood-ratio table. No clinical-history LR data available for BP5 assessment. Details ▾Hide ▴

Evidence considered

Variant absent from Li et al. 2020 BRCA2 clinical_history_LR table

Still missing

No clinical-history LR data for this variant

Sources

PMID:31853058 ↗31853058

Not applicable · 13· recorded as not applicable Show reasons ▾Hide reasons ▴

PS2 VCEPPS2 is not applicable for this VCEP per ClinGen ENIGMA BRCA1/2 specification v1.2. Details ▾Hide ▴

Sources

cspec ↗

PM1 VCEPPM1 is not applicable for this VCEP; captured by bioinformatic analysis (PP3/BP4) per ENIGMA BRCA2 specification. Details ▾Hide ▴

Sources

cspec ↗

PM2 N/APM2 is not applicable for deletion variants per ENIGMA BRCA2 specification v1.2: 'Do not apply for insertion, deletion or delins variants.' Details ▾Hide ▴

Evidence considered

Variant is a deletion
PM2 explicitly excluded by ENIGMA specification

Sources

cspec ↗

PM4 VCEPPM4 is not applicable for this VCEP per ENIGMA BRCA1/2 specification v1.2. Details ▾Hide ▴

Sources

cspec ↗

PM5 N/APM5 in ENIGMA BRCA2 is repurposed for PTC comparator logic (PM5_PTC). This intronic deletion at +11/+12 is not a protein termination codon variant and is not located in an exon. Details ▾Hide ▴

Evidence considered

Intronic variant
not a PTC
not in an exon with established pathogenic PTC comparators

Sources

cspec ↗

PM6 VCEPPM6 is not applicable for this VCEP per ENIGMA BRCA1/2 specification v1.2. Details ▾Hide ▴

Sources

cspec ↗

PP2 VCEPPP2 is not applicable for this VCEP per ENIGMA BRCA1/2 specification v1.2. Details ▾Hide ▴

Sources

cspec ↗

PP5 VCEPPP5 is not applicable for this VCEP per ClinGen Sequence Variant Interpretation VCEP Review Committee recommendation. Details ▾Hide ▴

Sources

cspec ↗

BP1 N/ABP1 applies to coding-region variants (silent, missense, in-frame indels). This is an intronic deletion at +11/+12, outside the coding region. Details ▾Hide ▴

Evidence considered

Intronic variant
not a coding-region variant type for BP1

Sources

cspec ↗

BP2 VCEPBP2 is not applicable for this VCEP per ENIGMA BRCA1/2 specification v1.2. Details ▾Hide ▴

Sources

cspec ↗

BP3 VCEPBP3 is not applicable for this VCEP; captured by bioinformatic tool prediction and domain analysis per ENIGMA specification. Details ▾Hide ▴

Sources

cspec ↗

BP6 VCEPBP6 is not applicable for this VCEP per ENIGMA BRCA1/2 specification v1.2. Details ▾Hide ▴

Sources

cspec ↗

PS5 N/APS5 is not applicable for this VCEP per ClinGen recommendations. Details ▾Hide ▴

Sources

cspec ↗

Identifiers

Gene: BRCA2
Transcript: NM_000059.4
Coding (HGVS c.): NM_000059.4:c.1909+11_1909+12del
Protein (HGVS p.): NP_000050.3:p.?
GRCh38: chr13:32333396 GTC>G
GRCh37: chr13:32907533 GTC>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…

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 — Select a row to find it on the plot; use the link to open its page.

	Protein	Location	Classification	Link

gnomAD v4.1 Allele count data not recorded

gnomAD v2.1 Allele count data not recorded

gnomAD-Canada v1.0 0 / 0 alleles AF 0 · 0 homozygotes · FAF 0

By genetic ancestry

gnomAD-Canada

AF 0 · 0 / 0 alleles · 0 hom

Statements

gnomAD v4.1

Absent from gnomAD v4.1.

gnomAD v2.1

Absent from gnomAD v2.1.

Open the gnomAD-Canada detail page →

SpliceAI and Pangolin

Pangolin splice lossmagnitude shown

-0.050

Pangolin splice gain

0.040

Other predictors

REVEL: Not available
BayesDel: Not available

How the predictions were used

Evidence considered

SpliceAI max delta = 0.00 ≤ 0.1
Intronic deletion at +11/+12
outside canonical +/-1
2 donor splice sites

Sources

spliceai ↗cspec ↗

Evidence considered

Intronic variant at +11 position
outside conserved donor motif (beyond +7)
BP4 met (SpliceAI max delta = 0.00 ≤ 0.1)

Sources

spliceai ↗cspec ↗

Evidence considered

SpliceAI max delta = 0.00
below ENIGMA PP3 threshold of ≥0.2

Sources

spliceai ↗cspec ↗

Statement

In silico

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

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.

gnomAD v4.1 Captured gnomAD v4.1 source record Open source ↗

gnomAD v2.1 Captured gnomAD v2.1 source record Open source ↗

SpliceAI Lookup Recorded maximum delta 0.000 Open source ↗

ClinVar Captured ClinVar source record Open source ↗

COSMIC Captured COSMIC source record Open source ↗

ClinGen CSpec Captured ClinGen CSpec source record Open source ↗

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

Absent from gnomAD v4.1.

gnomAD v2.1

Absent from gnomAD v2.1.

ClinVar

This variant is absent from ClinVar.

In silico

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

Somatic

This variant has not previously been reported in somatic cancers (COSMIC).