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ATRX
Final classification
VUS
ATRX c.3334A>G · p.Thr1112Ala
ATRX

NM_000489.5:c.3334A>G (p.Thr1112Ala) is a missense variant in ATRX, a chromatin remodeler gene associated with ATR-X syndrome and cancer predisposition. ATRX loss of function is an established germline disease mechanism.

Gene
ATRX
Transcript
NM_000489.5
HGVS · transcript:coding
NM_000489.5:c.3334A>G
Consequence
N/A
GRCh38
chrX:77681922 T>C
GRCh37
chrX:76937414 T>C
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 moderate, BP4 supporting benign; combination = 1 moderate + 1 supporting benign, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 moderate, BP4 supporting benign; combination = 1 moderate + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
ATRX c.3334A>G

NM_000489.5:c.3334A>G (p.Thr1112Ala) is a missense variant in ATRX, a chromatin remodeler gene associated with ATR-X syndrome and cancer predisposition. ATRX loss of function is an established germline disease mechanism.1 This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0 (PM2). It is also absent from ClinVar.2 Multiple in silico predictors suggest no damaging effect: BayesDel score is -0.527 (benign prediction) and SpliceAI predicts no splicing impact with a maximum delta score of 0.01 (BP4). REVEL score is not available.3 The variant has been reported in COSMIC (COSV64880047) with two somatic occurrences. No variant-specific functional studies, de novo reports, segregation data, or case-control evidence were identified. No functional data exist for this variant or a systematically characterized range that includes p.Thr1112. OncoKB classifies this variant as 'Unknown Oncogenic Effect.' No publications mention this exact variant.4 Applying generic ACMG/AMP 2015 combination rules: met criteria include PM2 (moderate) and BP4 (supporting benign). The evidence is conflicting with limited overall weight. No pathogenic criteria beyond PM2 are met, and BP4 provides supporting benign evidence. The variant is best classified as a Variant of Uncertain Significance.5

PM2 + BP4 VUS
1 pvs1_gene_context
3 bayesdelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_000489.5 · variants mapped to exon structure
ATRX NM_000489.5
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 21 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 moderate Pathogenic
This variant is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes), meeting the PM2 threshold of <0.1% allele frequency in population databases for non-VCEP assessment.
Absent from gnomAD v2.1v4.1and gnomAD-Canada v1.0 (AF = 0.0).
BP4 supporting Benign
Multiple lines of computational evidence suggest no damaging effect. BayesDel predicts a benign score of -0.527, and SpliceAI predicts no splicing impact (max delta score = 0.01). REVEL is not available. Two independent in silico tools support a benign interpretation.
BayesDel: -0.527 (benign prediction)SpliceAI max delta: 0.01 (no splice impact)REVEL: not found.
Assessed · not applied
Pathogenic
PS1 No known pathogenic variant with the same amino acid change (p.Thr1112Ala) has been reported in ClinVar or the literature.
PS2 No de novo data are available for this variant.
PS3 No functional data exist for this variant or a systematically characterized range that includes p.Thr1112.
PS4 No case-control or prevalence data are available.
PM1 The variant does not lie within a statistically significant mutational hotspot (cancerhotspots.org) and no functional domain characterization specifically identifying residue 1112 as critical was identified in the available evidence.
PM5 No same-residue pathogenic comparator variant was identified.
PM6 No de novo data are available.
PP1 No co-segregation data are available.
PP2 While ATRX loss of function is an established disease mechanism (ATR-X syndrome), the gene-level missense constraint data (e.g., missense Z-score) are not available in the evidence.
PP3 Multiple in silico tools do not support a deleterious effect.
PP4 No patient phenotype or clinical data were provided.
PP5 The variant is absent from ClinVar.
Benign
BA1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 The variant is absent from gnomAD v2.1 and v4.1.
BS2 No evidence of observation in healthy adults.
BS3 No functional studies demonstrating no damaging effect are available.
BS4 No segregation data are available.
BP1 ATRX missense variants are reported in association with ATR-X syndrome and cancer predisposition.
BP2 No phasing data are available.
BP5 No evidence that this variant has been found in a case with an alternate molecular basis for disease.
BP6 The variant is absent from ClinVar.
N/A · 5 PVS1 · PM3 · PM4 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). BayesDel score = -0.526868.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. ATRX, a tumor suppressor involved in transcriptional regulation, is infrequently altered in cancer.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV64880047, n = 2 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots