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TERT
Final classification
VUS
TERT c.875C>T · p.Thr292Met
TERT

NM_198253.2:c.875C>T (p.Thr292Met) is a missense variant in exon 2 of TERT. TERT is associated with autosomal dominant and recessive telomere biology disorders including dyskeratosis congenita, bone marrow failure, and pulmonary fibrosis.

Gene
TERT
Transcript
NM_198253.2
HGVS · transcript:coding
NM_198253.2:c.875C>T
Consequence
N/A
GRCh38
chr5:1294011 G>A
GRCh37
chr5:1294126 G>A
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 supporting, BP4 supporting; combination = 1 supporting + 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 supporting, BP4 supporting; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
TERT c.875C>T

NM_198253.2:c.875C>T (p.Thr292Met) is a missense variant in exon 2 of TERT. TERT is associated with autosomal dominant and recessive telomere biology disorders including dyskeratosis congenita, bone marrow failure, and pulmonary fibrosis.1 This variant is extremely rare in population databases, absent from gnomAD v2.1 and gnomAD-Canada, and present at an allele frequency of 6.3e-7 (1/1,586,736 alleles, 0 homozygotes) in gnomAD v4.1, satisfying PM2 at supporting strength.2 Multiple lines of computational evidence suggest this variant is tolerated: BayesDel score is -0.237 (benign range), REVEL score is 0.296 (below the 0.5 pathogenicity threshold), and SpliceAI predicts no splicing impact (max delta = 0.01), collectively satisfying BP4 at supporting strength.3 No functional studies, case-control data, segregation analysis, or de novo observations were identified for this variant. ClinVar reports two clinical laboratory submissions, both classifying the variant as Uncertain significance. All reviewed publications discuss TERT at the gene level and do not mention this specific variant.4 Under the generic ACMG/AMP 2015 classification framework, the variant NM_198253.2:c.875C>T (p.Thr292Met) is classified as a Variant of Uncertain Significance (VUS), with balanced pathogenic (PM2_supporting) and benign (BP4_supporting) evidence. Additional evidence such as functional characterization, segregation data, or case-control studies would be needed to reclassify this variant.5

PM2 + BP4 VUS
1 pvs1_gene_context
3 bayesdelrevelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_198253.2 · variants mapped to exon structure
TERT NM_198253.2
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 20 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is absent from gnomAD v2.1 and gnomAD-Canada v1.0, and is present at an extremely low frequency in gnomAD v4.1 (AF=6.3e-7, 1/1,586,736 alleles, 0 homozygotes). The highest subpopulation frequency is in South Asian (AF=1.14e-5). These frequencies are well below the 0.1% threshold for PM2 in genes associated with rare disease.
Absent from gnomAD v2.1.gnomAD v4.1: AF=6.3e-71/1
BP4 supporting Benign
Multiple lines of computational evidence suggest this variant is tolerated and does not impact gene product function. BayesDel predicts a benign score (-0.237), REVEL score is low (0.296, below the 0.5 threshold for deleterious prediction), and SpliceAI predicts no splicing impact (max delta = 0.01). The convergence of independent computational tools toward a benign prediction satisfies BP4 at supporting level.
BayesDel: -0.237 (benign prediction).REVEL: 0.296 (below 0.5 threshold).SpliceAI: max delta 0.01 (no predicted splice impact).
Assessed · not applied
Pathogenic
PS1 No evidence of a different nucleotide change at the same position (c.875) resulting in the same amino acid change (p.Thr292Met) that has been classified as pathogenic.
PS2 No de novo occurrence data are available for this variant.
PS3 No variant-specific functional studies have been identified for NM_198253.2:c.875C>T.
PS4 No significant enrichment of this variant in affected individuals compared to controls has been demonstrated.
PM1 The variant affects codon 292, which lies within the TEN (telomerase essential N-terminal) domain of TERT.
PM6 No de novo data are available for this variant.
PP1 No segregation data are available for this variant.
PP2 No gene-specific missense constraint data (HCI prior) are available for TERT.
PP3 Multiple in silico tools do not support a damaging effect for this variant.
PP4 No patient phenotype data are available to evaluate whether the clinical presentation is specific for TERT-related disease (telomere biology disorders including dyskeratosis congenita, bone marrow failure, pulmonary fibrosis).
PP5 This variant has been reported in ClinVar as Uncertain significance by two clinical laboratories (Labcorp/Invitae and Ambry Genetics).
Benign
BA1 The allele frequency in gnomAD v4.1 is 6.3e-7 (0.000063%), which is far below the 1% threshold required for BA1.
BS1 The allele frequency in gnomAD v4.1 is 6.3e-7 (0.000063%), which is far below the 0.3% threshold required for BS1.
BS2 Only one heterozygous carrier has been observed in gnomAD v4.1 (1/1,586,736 alleles, 0 homozygotes).
BS3 No well-established functional studies demonstrating no damaging effect have been identified for this variant.
BS4 No segregation data are available to evaluate lack of cosegregation with disease.
BP1 BP1 applies when a missense variant occurs in a gene where the primary disease mechanism is through truncating (loss-of-function) variants.
BP2 No evidence of this variant occurring in trans with a known pathogenic variant in TERT.
BP5 BP5 applies when a variant is found in a case with an alternate molecular basis for disease.
BP6 This variant is reported in ClinVar as Uncertain significance (VUS) by two clinical laboratories (Labcorp/Invitae and Ambry Genetics).
N/A · 3 PVS1 · PM5 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 6.30225e-07; MAF= 0.00006%, 1/1586736 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 1.14155e-05; MAF= 0.00114%, 1/87600 alleles, homozygotes = 0).
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
6.3e-05% · 1 / 1,586,736
0 hom
South Asian
1 / 87,600
0.0011%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American, European (non-Finnish))
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 has been reported in ClinVar as Uncertain significance (2 clinical laboratories). (ClinVarID = 1379490)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.296. BayesDel score = -0.237158.
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. TERT is an enzyme that functions to maintain telomere length and genomic stability. The TERT promoter is frequently mutated in various cancer types.
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; COSV99716364, 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
Triaged references · 3 PMIDs not cited in assessment
20301779 ↗ Dyskeratosis Congenita and Related Telomere Biology Disorders. CLINVAR
26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR
26389333 ↗ Genetics of Skin Cancer (PDQ®): Health Professional Version. CLINVAR