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c.*24339G>AUncertain significance
Print report
Variant interpretation report

c.*24339G>A

NM_001202543.1:c.*24339G>A View identifiers
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.

About the gene

No gene-level summary was recorded for this case.

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.

29 criteria with recorded statuses: 0 met · 16 not met · 3 not assessed · 10 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Pathogenic
PVS1PS1PS2PS3PS4PM1PM2PM3PM4PM5PM6PP1PP2PP3PP4PP5PS5
Benign
BA1BS1BS2BS3BS4BP1BP2BP3BP4BP5BP6BP7
Met Not met Not assessed Not applicable

NM_001202543.1:c.*24339G>A is a 3' UTR substitution in an unresolved gene. VariantValidator reports the coordinate is outside the bounds of the reference sequence, precluding gene-level normalization.

No population frequency data are available; gnomAD v2.1 and v4.1 returned null results, and gnomAD-Canada shows zero coverage (AC=0, AN=0) at this non-coding position.

No ClinVar entries, literature reports, functional studies, cosegregation data, or in silico predictions are available for this variant.

No ACMG/AMP pathogenic or benign criteria are met. The variant lacks sufficient evidence for any classification other than Uncertain Significance.

Not met · 16 · evaluated, threshold not reached

PS2 No de novo observation has been reported for NM_001202543.1:c.*24339G>A. No ClinVar submissions, literature reports, or family study data are available for this variant. Details ▾Hide ▴
Evidence considered
  • No de novo evidence in ClinVar (no submissions found).
  • No literature papers available for this variant.
Still missing
  • No family-based sequencing data available to assess de novo status.
PS3 No well-established in vitro or in vivo functional studies have been identified for NM_001202543.1:c.*24339G>A. No literature reports, OncoKB entries, or other curated functional evidence are available. Details ▾Hide ▴
Evidence considered
  • No functional study data found in literature_pass (0 PMIDs).
  • No OncoKB or COSMIC entries for this variant.
Still missing
  • Functional studies evaluating the impact of this 3' UTR variant on transcript stability
  • localization
  • or translation are absent.
PS4 No case-control or statistical evidence demonstrates enrichment of NM_001202543.1:c.*24339G>A in affected individuals. No ClinVar submissions, publications, or cohort data are available. Details ▾Hide ▴
Evidence considered
  • No ClinVar submissions or literature reports of this variant in affected individuals.
Still missing
  • No case-control or cohort data available to evaluate prevalence in disease.
PM1 No evidence places NM_001202543.1:c.*24339G>A in a mutational hotspot or well-established critical functional domain. The gene is unresolved and no domain mapping is available for this 3' UTR position. Details ▾Hide ▴
Evidence considered
  • Gene unresolved
  • no domain
  • hotspot
  • or functional region data available.
  • Hotspot assessment returned no match.
Still missing
  • Gene identification is required to assess whether the variant lies in a known functional domain.
PM6 No de novo observation with confirmed maternity/paternity has been reported for NM_001202543.1:c.*24339G>A. No literature or clinical submissions document a de novo event. Details ▾Hide ▴
Evidence considered
  • No de novo evidence in any source.
Still missing
  • No trio sequencing data available.
PP1 No cosegregation data are available for NM_001202543.1:c.*24339G>A. No family studies, linkage analyses, or segregation reports exist for this variant. Details ▾Hide ▴
Evidence considered
  • No cosegregation data in any source.
Still missing
  • No family-based genetic data available.
PP3 No in silico prediction tools support a deleterious effect for NM_001202543.1:c.*24339G>A. REVEL and BayesDel are not available for non-coding variants; no REVEL or BayesDel scores were returned. SpliceAI delta scores are null. Details ▾Hide ▴
Evidence considered
  • REVEL: not found (non-coding variant).
  • BayesDel: not found (non-coding variant).
  • SpliceAI: max_delta=null
  • no splicing impact predicted.
Still missing
  • In silico tools for non-coding variant interpretation (e.g.
  • CADD
  • Eigen
  • FATHMM-MKL) were not assessed.
PP4 No specific phenotype or family history data link NM_001202543.1:c.*24339G>A to disease. The gene is unresolved, and no clinical phenotype information is available in any source. Details ▾Hide ▴
Evidence considered
  • No phenotype data in ClinVar
  • literature
  • or clinical submissions.
Still missing
  • Proband phenotype and family history are unavailable.
PP5 No reputable source has classified NM_001202543.1:c.*24339G>A as pathogenic. ClinVar has no entry for this variant, and no literature reports a pathogenic classification. Details ▾Hide ▴
Evidence considered
  • ClinVar: no variation_id
  • no classification
  • no submissions.
BS2 No observation of NM_001202543.1:c.*24339G>A in a healthy adult in the homozygous state, hemizygous state, or in trans with a known pathogenic variant has been reported. No population genotype data are available. Details ▾Hide ▴
Evidence considered
  • No homozygous or hemizygous observations in gnomAD or ClinVar.
Still missing
  • Population genotype data for this non-coding position is unavailable.
BS3 No well-established functional studies demonstrate a neutral or benign effect for NM_001202543.1:c.*24339G>A. No in vitro or in vivo functional data are available for this variant. Details ▾Hide ▴
Evidence considered
  • No functional study data found in any source.
  • No literature papers available.
Still missing
  • Functional studies evaluating the 3' UTR variant's impact are absent.
BS4 No segregation data demonstrate lack of cosegregation with disease for NM_001202543.1:c.*24339G>A. No family studies are available. Details ▾Hide ▴
Evidence considered
  • No segregation or linkage data in any source.
Still missing
  • No family-based genetic data available.
BP2 No observation of NM_001202543.1:c.*24339G>A in trans with a known pathogenic variant has been reported. No phase-resolved genotype data are available. Details ▾Hide ▴
Evidence considered
  • No trans-phase observations in any data source.
Still missing
  • Phase-resolved genotype data are unavailable.
BP4 No in silico tools predict a benign or neutral effect for NM_001202543.1:c.*24339G>A. REVEL and BayesDel are unavailable for non-coding variants, and SpliceAI returns null scores. Computational evidence is insufficient to assign BP4. Details ▾Hide ▴
Evidence considered
  • REVEL: not found.
  • BayesDel: not found.
  • SpliceAI: max_delta=null.
Still missing
  • In silico tools appropriate for non-coding variant interpretation were not assessed.
BP5 No alternative molecular basis for disease has been identified in a case where NM_001202543.1:c.*24339G>A is present. No clinical context data are available. Details ▾Hide ▴
Evidence considered
  • No alternative molecular findings available in any source.
Still missing
  • Clinical context and alternative genetic findings are unavailable.
BP6 No reputable source has classified NM_001202543.1:c.*24339G>A as benign. ClinVar has no entry for this variant. Details ▾Hide ▴
Evidence considered
  • ClinVar: no variation_id
  • no classification
  • no submissions.

Not assessed · 3 · no assessment recorded

PM2 Population frequency data for NM_001202543.1:c.*24339G>A is unavailable. gnomAD v2.1 and v4.1 returned null results; gnomAD-Canada returned AC=0, AN=0 (zero coverage at this position). Since this is a deep 3' UTR variant, standard gnomAD calling does not cover this region. PM2 cannot be evaluated without population frequency data. Details ▾Hide ▴
Evidence considered
  • gnomAD v2.1: no data (null).
  • gnomAD v4.1: no data (null).
  • gnomAD-Canada: AC=0
  • AN=0 (no coverage at this non-coding position).
Still missing
  • Population frequency data for this non-coding position is not available through standard gnomAD resources. Alternative population databases or targeted sequencing of the 3' UTR region would be needed.
BA1 BA1 requires an allele frequency >1% in a reference population. Population frequency data for NM_001202543.1:c.*24339G>A is unavailable; gnomAD v2.1 and v4.1 returned null results, and gnomAD-Canada shows zero coverage (AC=0, AN=0). BA1 cannot be evaluated without frequency data. Details ▾Hide ▴
Evidence considered
  • gnomAD v2.1: no data.
  • gnomAD v4.1: no data.
  • gnomAD-Canada: AC=0
  • AN=0 (no coverage at this non-coding position).
Still missing
  • Population frequency data for this non-coding position is not available through standard gnomAD resources.
BS1 BS1 requires an allele frequency >0.3% in a reference population. As with BA1, population frequency data for this 3' UTR variant is unavailable through standard gnomAD resources. BS1 cannot be evaluated. Details ▾Hide ▴
Evidence considered
  • gnomAD v2.1: no data.
  • gnomAD v4.1: no data.
  • gnomAD-Canada: AC=0
  • AN=0 (no coverage at this non-coding position).
Still missing
  • Population frequency data for this non-coding position is not available through standard gnomAD resources.
Not applicable · 10· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ANM_001202543.1:c.*24339G>A is a 3' UTR substitution located 24,339 nucleotides downstream of the stop codon. This variant type is not predicted to cause loss of function via any PVS1-eligible null mechanism (nonsense, frameshift, canonical splice, initiation codon, or exon deletion) as defined by the ClinGen SVI PVS1 decision framework (PMC6185798). Additionally, the gene could not be resolved, so loss-of-function as a disease mechanism cannot be established. Details ▾Hide ▴
Evidence considered
  • Variant is in 3' UTR
  • not a null variant type eligible for PVS1.
  • pvs1_variant_assessment confirms variant_bucket='other' and apply_generic_pvs1_framework=false.
  • Gene-level LOF disease mechanism could not be established (gene unresolved).
Sources
pvs1_variant_assessmentpvs1_gene_contextpvs1_generic_framework ↗
PS1 N/APS1 requires the same amino acid change as an established pathogenic variant. This is a 3' UTR variant with no amino acid change; PS1 is not applicable to non-coding substitutions without protein consequence. Details ▾Hide ▴
Evidence considered
  • Variant is a 3' UTR substitution with no protein-level consequence.
PM3 N/APM3 applies to variants observed in trans with a pathogenic variant in recessive disorders. Gene and disease context are unresolved; this criterion cannot be assessed and is trivial for this case. Details ▾Hide ▴

No further detail was recorded.

PM4 N/APM4 applies to protein length changes from in-frame deletions/insertions in non-repeat regions. This variant is a single nucleotide substitution in the 3' UTR. Details ▾Hide ▴

No further detail was recorded.

PM5 N/APM5 requires a novel missense change at an amino acid residue where a different missense change is pathogenic. NM_001202543.1:c.*24339G>A is a 3' UTR variant with no amino acid change and no protein residue. PM5 candidate harvesting confirmed no eligible comparators. Details ▾Hide ▴
Evidence considered
  • pm5_candidates.json confirms pm5_mode='unknown'
  • eligible_for_classic_pm5_search=false.
  • Variant is 3' UTR
  • not coding
  • no residue-level comparator possible.
Sources
pm5_candidates
PP2 N/APP2 applies to missense variants in genes with a low rate of benign missense variation where missense is a known disease mechanism. NM_001202543.1:c.*24339G>A is a 3' UTR variant, not a missense change; PP2 is not applicable. Details ▾Hide ▴
Evidence considered
  • Variant is a 3' UTR substitution
  • not a missense variant.
BP1 N/ABP1 applies to missense variants in genes where a primarily truncating mechanism causes disease. NM_001202543.1:c.*24339G>A is a 3' UTR variant, not a missense change; BP1 is not applicable. Details ▾Hide ▴
Evidence considered
  • Variant is a 3' UTR substitution
  • not a missense variant.
BP3 N/ABP3 applies to in-frame deletions/insertions in non-repeat regions. This variant is a single nucleotide substitution in the 3' UTR. Details ▾Hide ▴

No further detail was recorded.

BP7 N/ABP7 applies to synonymous (silent) variants for which splicing algorithms predict no impact and the nucleotide is not highly conserved. NM_001202543.1:c.*24339G>A is a 3' UTR variant, not a synonymous coding change; BP7 is not applicable. Details ▾Hide ▴
Evidence considered
  • Variant is a 3' UTR substitution
  • not a synonymous coding variant.
PS5 N/APS5 requires a novel missense variant at the same amino acid residue as another pathogenic missense, with very strong supporting evidence. This is a 3' UTR variant with no amino acid change; PS5 is not applicable. Details ▾Hide ▴
Evidence considered
  • Variant is a 3' UTR substitution
  • no protein residue affected.

Identifiers

Coding (HGVS c.)
NM_001202543.1:c.*24339G>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.

Open the gnomAD-Canada detail page →

Other predictors

REVEL
Not available
BayesDel
Not available

How the predictions were used

PP3 No in silico prediction tools support a deleterious effect for NM_001202543.1:c.*24339G>A. REVEL and BayesDel are not available for non-coding variants; no REVEL or BayesDel scores were returned. SpliceAI delta scores are null. Details ▾Hide ▴
Evidence considered
  • REVEL: not found (non-coding variant).
  • BayesDel: not found (non-coding variant).
  • SpliceAI: max_delta=null
  • no splicing impact predicted.
Still missing
  • In silico tools for non-coding variant interpretation (e.g.
  • CADD
  • Eigen
  • FATHMM-MKL) were not assessed.
BP4 No in silico tools predict a benign or neutral effect for NM_001202543.1:c.*24339G>A. REVEL and BayesDel are unavailable for non-coding variants, and SpliceAI returns null scores. Computational evidence is insufficient to assign BP4. Details ▾Hide ▴
Evidence considered
  • REVEL: not found.
  • BayesDel: not found.
  • SpliceAI: max_delta=null.
Still missing
  • In silico tools appropriate for non-coding variant interpretation were not assessed.
BP7 N/ABP7 applies to synonymous (silent) variants for which splicing algorithms predict no impact and the nucleotide is not highly conserved. NM_001202543.1:c.*24339G>A is a 3' UTR variant, not a synonymous coding change; BP7 is not applicable. Details ▾Hide ▴
Evidence considered
  • Variant is a 3' UTR substitution
  • not a synonymous coding variant.

0 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata.