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LYFE SCIENCES
Project: HERA
NM_002439.5:c.2436-13G>T
p.?  ·  MSH3
ACMG/AMP
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Classification rationale
1

The MSH3 c.2436-13G>T (p.?) variant has been reported in ClinVar as Likely benign.

clinvar ↗
2

This variant is present in population databases, including gnomAD v2.1 at 0.07852% overall with a highest observed population frequency of 0.14797% and gnomAD v4.1 at 0.13248% overall with a highest observed population frequency of 0.17028%, which is above a default PM2 rarity threshold of 0.1% but below default BS1 and BA1 thresholds.

gnomad_v2 ↗ gnomad_v4 ↗
3

In silico splicing prediction does not support a damaging splice effect, with SpliceAI showing a maximum delta score of 0.02.

spliceai ↗
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
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Rule
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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= 0.000785157; MAF= 0.07852%, 222/282746 alleles, homozygotes = 1) and has highest observed frequency in the European (non-Finnish) population (AF= 0.00147968; MAF= 0.14797%, 191/129082 alleles, homozygotes = 1); grpmax FAF= 0.00136914.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 0.00132477; MAF= 0.13248%, 2106/1589706 alleles, homozygotes = 5) and has highest observed frequency in the European (non-Finnish) population (AF= 0.00170283; MAF= 0.17028%, 1972/1158070 alleles, homozygotes = 5); grpmax FAF= 0.00164017.
gnomAD v2 ↗ gnomAD v4 ↗
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Likely benign (3 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 = 0.02).
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.