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LYFE SCIENCES
Project: HERA
NM_021946.4:c.4464C>T
p.Asp1488=  ·  BCORL1
ACMG/AMP
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Classification rationale
1

The BCORL1 NM_021946.4:c.4464C>T (p.Asp1488=) variant has not been reported in ClinVar.

clinvar ↗
2

This variant is present at low frequency in gnomAD, with overall allele frequencies of 0.00396% in v2.1 and 0.00399% in v4.1; the highest observed subpopulation frequency is 0.04636% in gnomAD v4.1, which is below the 0.1% PM2 threshold and below the 0.3% BS1 threshold used here.

gnomad_v2 ↗ gnomad_v4 ↗
3

Computational splice prediction does not support a damaging effect, as SpliceAI predicts no significant splice impact with a maximum delta score of 0.01, and the variant-level splice assessment indicates that this synonymous change is not in a canonical splice-site position.

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
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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= 3.95514e-05; MAF= 0.00396%, 7/176985 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 0.000169367; MAF= 0.01694%, 3/17713 alleles, homozygotes = 0); grpmax FAF= 4.577e-05.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 3.98855e-05; MAF= 0.00399%, 48/1203445 alleles, homozygotes = 0) and has highest observed frequency in the Middle Eastern population (AF= 0.000463607; MAF= 0.04636%, 2/4314 alleles, homozygotes = 0); grpmax FAF= 0.00011029.
gnomAD v2 ↗ gnomAD v4 ↗
ClinVar evidence
02
ClinVar
This variant is absent from ClinVar.
ClinVar ↗
Functional evidence
03
Functional
OncoKB: Unknown Oncogenic Effect
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
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 does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV54397317, n = 5 times).
COSMIC ↗
Cancer hotspots evidence
06
Cancer hotspots Not found
This variant does not lie in a statistically significant hotspot.
ResidueD1488
Hotspots ↗