Back
LYFE SCIENCES
Project: HERA
NM_000179.3:c.4002-17T>C
p.?  ·  MSH6
Starting
Initialising…
0%
Legacy Engine
Processing…
Classification rationale
1

The MSH6 c.4002-17T>C (NP_000170.1:p.?) variant has not been observed in somatic cancers in COSMIC and has not been reported in ClinVar.

clinvar ↗
2

This variant is absent from gnomAD v4.1, gnomAD v2.1, and gnomAD-Canada, supporting rarity below the MSH6 PM2 threshold of less than 0.00002.

gnomad_v4 ↗ gnomad_v2 ↗ gnomad_canada ↗ cspec ↗
3

SpliceAI predicts no significant splice impact, with a maximum delta score of 0.04, which is below the MSH6 BP4 threshold of less than or equal to 0.1 and below the PP3 threshold of greater than or equal to 0.2 for non-canonical splice variants.

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
ClinVar evidence
02
ClinVar
This variant is absent from ClinVar.
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 = 0.04).
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.