Back
LYFE SCIENCES
Project: HERA
NM_000251.3:c.1661+1G>A
p.?  ·  MSH2
Starting
Initialising…
0%
Legacy Engine
Ready
View Legacy →
Classification rationale
1

The MSH2 NM_000251.3:c.1661+1G>A (NP_000242.1:p.?) variant has been reported in ClinVar, including an InSiGHT expert panel classification of likely pathogenic and additional pathogenic/likely pathogenic clinical laboratory submissions.

clinvar ↗
2

This variant is absent from gnomAD v2.1 and is present only once in gnomAD v4.1 (1/1,612,780 alleles; AF 6.20e-07), which is below the MSH2 VCEP PM2 threshold of 0.00002.

gnomad_v2 ↗ gnomad_v4 ↗ cspec ↗
3

SpliceAI predicts a strong splice effect for this canonical donor variant (max delta score 0.97), supporting predicted disruption of normal splicing; however, this computational evidence was not counted separately because the same splice effect is captured under PVS1 for a canonical +1 splice-site variant.

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
—
—
Rationale
Select a criterion to inspect its explanation.
Evidence used
  • —
Gaps remaining
  • —
Rule
—
Publications
—
Research and evidence
gnomAD v2.1 evidence
v2.1
gnomAD v4.1 evidence
v4.1
01
Population
gnomAD v2.1Absent from gnomAD v2.1.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 6.20047e-07; MAF= 0.00006%, 1/1612780 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.48089e-07; MAF= 0.00008%, 1/1179122 alleles, homozygotes = 0).
gnomAD v2 ↗ gnomAD v4 ↗
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Pathogenic (4 clinical laboratories) and as Likely pathogenic (2 clinical laboratories) and as Likely pathogenic by International Society for Gastrointestinal Hereditary Tumours (InSiGHT) (expert panel).
ClinVar ↗
03
Functional
No functional summary recorded.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 0.97). BayesDel score = 0.66.
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.