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LYFE SCIENCES
Project: HERA
NM_024675.4:c.1058A>T
p.Lys353Ile  ·  PALB2
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Classification rationale
1

The PALB2 c.1058A>T (p.Lys353Ile) variant has been reported in ClinVar as uncertain significance by a single submitter.

clinvar ↗
2

This variant is absent from gnomAD v2.1 and gnomAD v4.1, and its gnomAD v4.1 allele frequency is therefore below the PALB2 PM2_Supporting threshold of 0.000333%.

cspec ↗ gnomad_v2 ↗ gnomad_v4 ↗
3

PALB2-specific rules support BP1 for this missense variant, while SpliceAI predicts no significant splice impact with a maximum delta score of 0.00 and PVS1, PP3, and BP4 are not applied in this missense setting.

cspec ↗ 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
  • —
Rule
—
Publications
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Research and evidence
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory).
ClinVar ↗
Functional evidence
03
Functional
OncoKB: Unknown Oncogenic Effect
OncoKB has not reviewed this specific variant; no variant-level oncogenicity or biological effect is available. Gene-level context: PALB2, a scaffolding protein involved in DNA repair, is altered in various cancers.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.086. BayesDel score = -0.4788.
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
COSMIC ↗
Cancer hotspots evidence
06
Cancer hotspots Not found
This variant does not lie in a statistically significant hotspot.
ResidueK353
Hotspots ↗