Genetic Information

Gene & Transcript Details

Gene
BRCA2
Transcript
NM_000059.3 MANE Select
Total Exons
—
Reference Sequence
NC_000013.10
Alternative Transcripts
IDStatusDetails
NM_000059.4 MANE Select 11954 nt | 200–10456
NM_000059.2 Alternative 11386 nt | 228–10484
NM_000059.3 RefSeq Select 11386 nt | 228–10484

Variant Details

HGVS Notation
NM_000059.3:c.68-7del
Protein Change
?
Location
Exon 2 (Exon 2 of )
2
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers
—

Clinical & Population Data

Population Frequency

gnomAD
Global Frequency
0.0847 in 100,000
Extremely Rare
ACMG Criteria Applied PM2
This variant is absent or extremely rare in population databases (PM2 criteria applies).

ClinVar

Open
Classification
Uncertain Significance (VUS)
2 publications
Publications List
Clinical Statement

"This variant has been reported in ClinVar as Benign (5 clinical laboratories) and as Uncertain significance (3 clinical laboratories) and as Benign by ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen expert panel."

COSMIC Somatic Evidence

Open
COSMIC ID
COSN28852724
Recurrence
8 occurrences
PM1 Criteria
Not Applied
COSMIC Database Preview
COSMIC Preview
Accessing full COSMIC database details requires institutional login or subscription.

Functional Impact & Domains

Functional Domain

Hotspot Status
Not a hotspot
Domain Summary
This variant is not located in a mutational hotspot or critical domain.
Related Variants in This Domain
No evidence of other pathogenic variants at this position in gene BRCA2.

Functional Studies & Therapeutic Relevance

Functional Summary

Error in OpenAI Consolidation. OncoKB: BRCA268-7delBRCA268-7delSomaticNCBI Gene:675|Show additional gene information Variant OverviewBRCA2, a tumor suppressor involved in the DNA damage response, is mutated in various cancer types.The BRCA2 68-7del alteration has not specifically been reviewed by the OncoKB team, and therefore its biological significance is unknown. JAX-CKB: No results found

Database Previews
OncoKB
OncoKB Preview
JAX-CKB
JAX-CKB Preview

Click on previews to view full database entries. External databases may require institutional access.

Computational Analysis

Pathogenicity Predictions

SpliceAI
Predictor Consensus
Unknown
PP3 Applied
No
REVEL Score
0.0
Threshold: ≥0.75 = PP3 applied

SpliceAI Scores

Window: ±500bp
Effect Type Score Position
- Acceptor Loss (AL) 0.04 17 bp
- Donor Loss (DL) 0.02 265 bp
+ Acceptor Gain (AG) 0.0 23 bp
+ Donor Gain (DG) 0.0 -306 bp
High impact (≥0.5) Medium impact (0.2-0.49) Low impact (<0.2)

VCEP Guidelines

Applied ACMG/AMP Criteria (VCEP Specific)

Filter Criteria:
PM2

PM2 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)

BP4

BP4 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)