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NM_001202543.1:c.*25175G>A
ACMG/AMP
0%
complete
Final classification
VUS
c.*25175G>A
This variant

The NM_001202543.1:c.*25175G>A variant could not be assigned to a validated gene, genomic coordinate, or protein consequence, so somatic cancer and germline disease database observations were not established.

Transcript
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HGVS · transcript:coding
NM_001202543.1:c.*25175G>A
GRCh38
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GRCh37
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gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: none; combination = no applied criteria, which maps to VUS.
Classification rationale
VUS
c.*25175G>A

The NM_001202543.1:c.*25175G>A variant could not be assigned to a validated gene, genomic coordinate, or protein consequence, so somatic cancer and germline disease database observations were not established. Population frequency could not be evaluated because a validated genomic representation was not available for gnomAD-based review. No published functional evidence establishing either a damaging or benign effect was identified, and gene-level loss-of-function context remained unresolved for PVS1 consideration.1 SpliceAI, REVEL, and BayesDel results were not available for this variant representation, so computational evidence could not support either PP3 or BP4.

1 pvs1_gene_contextpvs1_variant_assessment
LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
Applied criteria · 0 applied · 20 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 0

No criteria were applied for this variant.

Assessed · not applied · 0 not met · 20 not assessed
Pathogenic
PVS1 This variant description does not have a validated gene assignment or transcript-bounded consequence, and germline loss-of-function disease mechanism could not be established for PVS1 use.
PS2 No confirmed de novo data were identified for this variant, so PS2 is not assessed.
PS3 No published functional study establishing a damaging effect for this variant was identified, so PS3 is not assessed.
PS4 Case-control or prevalence data showing enrichment in affected individuals were not identified, so PS4 is not assessed.
PM2 Population frequency could not be established because no validated genomic coordinates were available for gnomAD-based review, so PM2 is not assessed.
PM3 No allelic-phase or recessive case evidence was identified for this variant, so PM3 is not assessed.
PM6 No assumed de novo evidence without full parental confirmation was identified for this variant, so PM6 is not assessed.
PP1 No segregation data were identified for this variant, so PP1 is not assessed.
PP3 Computational evidence could not be established because SpliceAI, REVEL, and BayesDel results were not available for a validated genomic representation of this variant.
PP4 No phenotype-specific evidence linking this variant to a highly specific monogenic presentation was identified, so PP4 is not assessed.
PP5 No established pathogenic assertion from a qualifying external source was identified for this variant, so PP5 is not assessed.
Benign
BA1 A population frequency high enough for BA1 could not be evaluated because no validated genomic coordinates were available.
BS1 Population frequency relative to a benign threshold could not be evaluated because no validated genomic coordinates were available.
BS2 No evidence showing this variant in healthy individuals at a frequency inconsistent with disease was identified, so BS2 is not assessed.
BS3 No published functional study showing no damaging effect for this variant was identified, so BS3 is not assessed.
BS4 No non-segregation data were identified for this variant, so BS4 is not assessed.
BP2 No phase data showing this variant with another pathogenic variant in a configuration supporting BP2 were identified, so BP2 is not assessed.
BP4 Computational evidence supporting no impact was not available because SpliceAI, REVEL, and BayesDel results were not established for a validated genomic representation of this variant.
BP5 No evidence was identified showing that an alternate molecular cause fully explains the phenotype while this variant is present, so BP5 is not assessed.
BP6 No qualifying external benign assertion was identified for this variant, so BP6 is not assessed.
N/A · 8 PS1 · PM1 · PM4 · PM5 · PP2 · BP1 · BP3 · BP7
Research & evidence
Population frequency
v4.1
This variant is absent from gnomAD v4.1.
v2.1
This variant is absent from gnomAD v2.1.
🇨🇦 CA
This variant is absent from gnomAD-Canada.
Allele frequency by ancestry
three datasets · side by side
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD 🇨🇦 ↗
ClinVar No data
No ClinVar submissions were recorded for this variant.
In silico No data
No in-silico prediction was recorded for this variant.
Functional No data
No calibrated functional assay or RNA evidence was identified for this variant.
Somatic evidence
COSMIC
This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant cancer hotspot.
Sources & reference links

No sources recorded.