About the gene
No gene-level summary was recorded for this case.
Previous versions
Classification
Uncertain significance
Variant description:
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.
Uncertain.The recorded classification is uncertain significance.
In plain language
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.
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.
01The reasoning
How it was classified
The recorded framework is Not recorded. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
Recorded applied criteria
The applied criteria and their strengths are shown as assessed under the stated framework.
Pathogenic evidence criteria: 0
Benign evidence criteria: 0
Pathogenic criteria applied · 0
No pathogenic criterion marked as applied in the recorded assessment.
Benign criteria applied · 0
No benign criterion marked as applied in the recorded assessment.
Recorded classification: Uncertain significance
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.
02The sources
Evidence at a glance
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
No screenshot for this evidence
Population frequency
Not recorded
gnomAD v4.1 allele counts were not recorded for this variant.
No listed criterion applied
gnomAD-Canada ↗
No screenshot for this evidence
Computational predictions
Not recorded
No SpliceAI or REVEL score is recorded in the fields used for this tile.
No listed criterion applied
No screenshot for this evidence
ClinVar submissions
Not recorded
A ClinVar laboratory submission summary was not recorded.
Context only
No screenshot for this evidence
Functional evidence
Not recorded
No standalone functional evidence summary is recorded in evidence_summary.functional.
No listed criterion applied
No screenshot for this evidence
Somatic evidence
Not assessed
No COSMIC evidence statement is recorded in this case.
Context only
For specialists
Technical detail
ACMG/AMP criteria under Not recorded, with the data and sources behind each one.
28 criteria with recorded statuses: 0 met · 0 not met · 20 not assessed · 8 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
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.
SpliceAI, REVEL, and BayesDel results were not available for this variant representation, so computational evidence could not support either PP3 or BP4.
No criteria match.
Not assessed · 20 · no assessment recorded
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. Available evidence does not support applying generic PVS1 at this time. Details ▾Hide ▴
Evidence considered
- PVS1 gene gate is manual_review_required
- Generic PVS1 scaffold indicates apply_generic_pvs1_framework=false
Still missing
- Validated gene assignment
- Confirmed transcript consequence
- Gene-specific or disease-specific loss-of-function mechanism evidence
Sources
PS2 No confirmed de novo data were identified for this variant, so PS2 is not assessed. Details ▾Hide ▴
Still missing
- Documented maternity and paternity-confirmed de novo evidence
PS3 No published functional study establishing a damaging effect for this variant was identified, so PS3 is not assessed. Details ▾Hide ▴
Still missing
- Variant-specific well-established functional data
PS4 Case-control or prevalence data showing enrichment in affected individuals were not identified, so PS4 is not assessed. Details ▾Hide ▴
Still missing
- Affected-vs-control enrichment data
- Multiple well-documented affected observations
PM2 Population frequency could not be established because no validated genomic coordinates were available for gnomAD-based review, so PM2 is not assessed. Details ▾Hide ▴
Evidence considered
- No chromosomal coordinates available
Still missing
- Validated genomic coordinates
- Population frequency across reference datasets
PM3 No allelic-phase or recessive case evidence was identified for this variant, so PM3 is not assessed. Details ▾Hide ▴
Still missing
- Confirmed trans observations in an appropriate recessive disease context
PM6 No assumed de novo evidence without full parental confirmation was identified for this variant, so PM6 is not assessed. Details ▾Hide ▴
Still missing
- Documented assumed de novo evidence
PP1 No segregation data were identified for this variant, so PP1 is not assessed. Details ▾Hide ▴
Still missing
- Family segregation evidence
PP3 Computational evidence could not be established because SpliceAI, REVEL, and BayesDel results were not available for a validated genomic representation of this variant. PP3 is not assessed. Details ▾Hide ▴
Evidence considered
- SpliceAI not established
- REVEL skipped
- BayesDel skipped
Still missing
- Validated genomic coordinates
- Available in silico prediction scores
PP4 No phenotype-specific evidence linking this variant to a highly specific monogenic presentation was identified, so PP4 is not assessed. Details ▾Hide ▴
Still missing
- Detailed phenotype with gene-disease specificity
PP5 No established pathogenic assertion from a qualifying external source was identified for this variant, so PP5 is not assessed. Details ▾Hide ▴
Still missing
- Qualifying external classification with accessible supporting basis
BA1 A population frequency high enough for BA1 could not be evaluated because no validated genomic coordinates were available. BA1 is not assessed. Details ▾Hide ▴
Evidence considered
- No chromosomal coordinates available
Still missing
- Validated genomic coordinates
- Population frequency in reference datasets
BS1 Population frequency relative to a benign threshold could not be evaluated because no validated genomic coordinates were available. BS1 is not assessed. Details ▾Hide ▴
Evidence considered
- No chromosomal coordinates available
Still missing
- Validated genomic coordinates
- Population frequency in reference datasets
BS2 No evidence showing this variant in healthy individuals at a frequency inconsistent with disease was identified, so BS2 is not assessed. Details ▾Hide ▴
Still missing
- Unaffected adult observations in an appropriate disease context
BS3 No published functional study showing no damaging effect for this variant was identified, so BS3 is not assessed. Details ▾Hide ▴
Still missing
- Variant-specific well-established benign functional data
BS4 No non-segregation data were identified for this variant, so BS4 is not assessed. Details ▾Hide ▴
Still missing
- Family data demonstrating lack of segregation
BP2 No phase data showing this variant with another pathogenic variant in a configuration supporting BP2 were identified, so BP2 is not assessed. Details ▾Hide ▴
Still missing
- Allelic phase data in an appropriate disease context
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. BP4 is not assessed. Details ▾Hide ▴
Evidence considered
- SpliceAI not established
- REVEL skipped
- BayesDel skipped
Still missing
- Validated genomic coordinates
- Available in silico prediction scores
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. Details ▾Hide ▴
Still missing
- Documented alternate molecular diagnosis
BP6 No qualifying external benign assertion was identified for this variant, so BP6 is not assessed. Details ▾Hide ▴
Still missing
- Qualifying external benign classification with accessible supporting basis
Not applicable · 8· recorded as not applicable Show reasons ▾Hide reasons ▴
PS1 N/AThis submitted variant is described in the 3' untranslated region and does not define an amino acid substitution, so same-amino-acid-change evidence under PS1 is not applicable. Details ▾Hide ▴
Evidence considered
- Submitted HGVS uses c.* notation
PM1 N/AThis submitted variant is not a protein-altering missense change with an established critical residue or functional domain, so PM1 is not applicable. Details ▾Hide ▴
Evidence considered
- No protein consequence available
PM4 N/AThis variant is not an in-frame protein length change, so PM4 is not applicable. Details ▾Hide ▴
Evidence considered
- No protein length alteration described
PM5 N/AThis submitted variant does not define a missense residue change, and same-residue missense comparator logic could not be applied. PM5 is not applicable. Details ▾Hide ▴
Evidence considered
- PM5 mode unknown
- eligible_for_classic_pm5_search=false
Sources
pm5_candidates
PP2 N/AThis submitted variant is not a missense change, so PP2 is not applicable. Details ▾Hide ▴
Evidence considered
- No missense consequence available
BP1 N/AThis submitted variant is not a missense change, so BP1 is not applicable. Details ▾Hide ▴
Evidence considered
- No missense consequence available
BP3 N/AThis variant is not an in-frame change in a repetitive region without known function, so BP3 is not applicable. Details ▾Hide ▴
Evidence considered
- No in-frame protein change described
BP7 N/ABP7 applies to synonymous or certain intronic variants without predicted splice impact. This submitted 3' untranslated region variant does not meet that criterion definition, so BP7 is not applicable. Details ▾Hide ▴
Evidence considered
- Submitted HGVS uses c.* notation
Identifiers
- Coding (HGVS c.)
- NM_001202543.1:c.*25175G>A
gnomAD v4.1
Allele count data not recorded
gnomAD v2.1
Allele count data not recorded
gnomAD-Canada v1.0
0 / 0 alleles
AF 0 · 0 homozygotes · FAF 0
By genetic ancestry
gnomAD-Canada
AF 0 · 0 / 0 alleles · 0 hom
Statements
No population statements were recorded.
Other predictors
- REVEL
- Not available
- BayesDel
- Not available
How the predictions were used
PP3 Computational evidence could not be established because SpliceAI, REVEL, and BayesDel results were not available for a validated genomic representation of this variant. PP3 is not assessed. Details ▾Hide ▴
Evidence considered
- SpliceAI not established
- REVEL skipped
- BayesDel skipped
Still missing
- Validated genomic coordinates
- Available in silico prediction scores
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. BP4 is not assessed. Details ▾Hide ▴
Evidence considered
- SpliceAI not established
- REVEL skipped
- BayesDel skipped
Still missing
- Validated genomic coordinates
- Available in silico prediction scores
BP7 N/ABP7 applies to synonymous or certain intronic variants without predicted splice impact. This submitted 3' untranslated region variant does not meet that criterion definition, so BP7 is not applicable. Details ▾Hide ▴
Evidence considered
- Submitted HGVS uses c.* notation
0 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata.