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LYFE SCIENCES
Project: HERA
NM_000059.4:c.682-30A>C
p.?  ·  BRCA2
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Initialising…
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Legacy Engine
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Classification rationale
1

The BRCA2 c.682-30A>C (p.?) variant has been reported in ClinVar as benign by 2 clinical laboratories and likely benign by 2 clinical laboratories.

clinvar ↗
2

This variant is present in gnomAD with a group maximum filter allele frequency of 0.00539635 in v2.1 and 0.00494792 in v4.1, both above the ENIGMA BRCA2 BA1 threshold of 0.001 and the BS1 strong threshold of 0.0001.

gnomad_v2 ↗ gnomad_v4 ↗ cspec ↗
3

SpliceAI predicts no significant splice impact for this intronic variant, with a maximum delta score of 0.01, which supports BP4 and BP7 under the ENIGMA BRCA2 splicing rules.

spliceai ↗ cspec ↗
Applied criteria
Met
Not met
Not assessed
N/A
Very strong
Strong
Moderate
Supporting
Pathogenic evidence
PVS
PVS1
PS
PS1
PS2
PS3
PS4
PM
PM1
PM2
PM3
PM4
PM5
PM6
PP
PP1
PP2
PP3
PP4
PP5
Benign evidence
BA
BA1
BS
BS1
BS2
BS3
BS4
BP
BP1
BP2
BP3
BP4
BP5
BP6
BP7
PVS1
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Rationale
Select a criterion to inspect its explanation.
Evidence used
  • —
Gaps remaining
  • —
Rule
—
Publications
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Research and evidence
gnomAD v2.1 evidence
v2.1
gnomAD v4.1 evidence
v4.1
01
Population
gnomAD v2.1This variant is present in gnomAD v2.1 (AF= 0.000536223; MAF= 0.05362%, 136/253626 alleles, homozygotes = 1) and has highest observed frequency in the African/African American population (AF= 0.0060639; MAF= 0.60639%, 134/22098 alleles, homozygotes = 1); grpmax FAF= 0.00539635.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 0.000289734; MAF= 0.02897%, 391/1349516 alleles, homozygotes = 1) and has highest observed frequency in the African/African American population (AF= 0.00539895; MAF= 0.53989%, 375/69458 alleles, homozygotes = 1); grpmax FAF= 0.00494792.
gnomAD v2 ↗ gnomAD v4 ↗
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Benign (2 clinical laboratories) and as Likely benign (2 clinical laboratories).
ClinVar ↗
03
Functional
No functional summary recorded.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant has not previously been reported in somatic cancers (COSMIC).
COSMIC ↗
06
Cancer hotspots
No cancer hotspot summary recorded.