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TERT
Final classification
VUS
TERT c.2509C>T · p.Leu837Phe
TERT

NM_198253.2:c.2509C>T (p.Leu837Phe) is a rare missense variant in the TERT gene that is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada (PM2_Supporting).

Gene
TERT
Transcript
NM_198253.2
HGVS · transcript:coding
NM_198253.2:c.2509C>T
Consequence
N/A
GRCh38
chr5:1268593 G>A
GRCh37
chr5:1268708 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; combination = 1 supporting, 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; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
TERT c.2509C>T

NM_198253.2:c.2509C>T (p.Leu837Phe) is a rare missense variant in the TERT gene that is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada (PM2_Supporting).1 This variant has been reported in ClinVar as a Variant of Uncertain Significance by a single clinical laboratory (Labcorp/Invitae, SCV003459151).2 No variant-specific functional studies, case-control data, de novo observations, segregation data, or same-residue pathogenic comparators were identified for this variant.3 In silico predictions are conflicting: REVEL predicts a deleterious effect (0.735), while BayesDel predicts a benign effect (0.123), and SpliceAI predicts no splicing impact (delta = 0.00).4 TERT loss-of-function is an established disease mechanism for autosomal dominant dyskeratosis congenita and related telomere biology disorders, and both truncating and missense variants have been reported as pathogenic in the literature.5 Applying generic ACMG/AMP 2015 classification rules (PMID:25741868), only one supporting criterion (PM2) is met, with no benign criteria met. This is insufficient to classify as Likely Pathogenic or Likely Benign, resulting in a final classification of Variant of Uncertain Significance (VUS).6

PM2 VUS
3 oncokb ↗pm5_candidates
4 revelbayesdelspliceai ↗
5 pvs1_gene_context
6 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 · 1 applied · 22 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_198253.2:c.2509C>T is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes), meeting PM2 at supporting strength under generic ACMG/AMP with an allele frequency of 0.0 in all population databases.
Absent from gnomAD v2.1 (exome).Absent from gnomAD v4.1 (exome).Absent from gnomAD-Canada v1.0 (genome
Assessed · not applied
Pathogenic
PS1 No pathogenic or likely pathogenic variant with the same amino acid change (p.Leu837Phe or another change at L837) was identified in ClinVar or the literature.
PS2 No de novo observation (with confirmed maternity and paternity) was identified for NM_198253.2:c.2509C>T in the available evidence.
PS3 No variant-specific functional data were identified for NM_198253.2:c.2509C>T (p.Leu837Phe) in the literature or through OncoKB.
PS4 No case-control data or statistically significant enrichment of NM_198253.2:c.2509C>T in affected individuals over controls was identified.
PM1 The variant p.Leu837Phe lies in the C-terminal region of TERT but is not located in a statistically significant mutational hotspot per cancerhotspots.org, and no literature was identified that specifically characterizes position 837 as lying within a well-characterized critical functional domain where missense variants are an established disease mechanism.
PM5 No pathogenic or likely pathogenic missense variant at the same amino acid residue (p.Leu837) was identified in ClinVar.
PM6 No de novo observation (without confirmed parentage) was identified for NM_198253.2:c.2509C>T in the available evidence.
PP1 No co-segregation data with disease in multiple affected family members were identified for this variant.
PP2 PP2 requires evidence that TERT has a low rate of benign missense variation (e.g., high missense Z-score or constraint metric).
PP3 In silico predictions are conflicting: REVEL predicts a deleterious effect (score 0.735, above 0.5 threshold), but BayesDel predicts a benign effect (score 0.123, below the damaging threshold).
PP4 No patient-specific phenotype or family history data highly specific for a TERT-related telomere biology disorder were available for this case.
PP5 No reputable source classifies NM_198253.2:c.2509C>T as pathogenic.
Benign
BA1 NM_198253.2:c.2509C>T is absent from all population databases (gnomAD v2.1, v4.1, gnomAD-Canada).
BS1 NM_198253.2:c.2509C>T is absent from all population databases.
BS2 No evidence that NM_198253.2:c.2509C>T has been observed in a healthy adult individual for a fully penetrant disorder.
BS3 No well-established functional studies were identified that demonstrate NM_198253.2:c.2509C>T has no deleterious effect on protein function or splicing.
BS4 No segregation data in affected families are available to demonstrate lack of co-segregation with disease.
BP1 While TERT loss-of-function is an established disease mechanism for telomere biology disorders, pathogenic missense variants in TERT are also well-documented in the literature (e.g., in dyskeratosis congenita and MDS).
BP2 No evidence that NM_198253.2:c.2509C>T has been observed in trans with a known dominant pathogenic variant for a fully penetrant disorder.
BP4 In silico predictions are conflicting: REVEL score of 0.735 suggests a deleterious effect, which contradicts the benign prediction from BayesDel (score 0.123).
BP5 No evidence that NM_198253.2:c.2509C>T was found in a case with an alternative molecular basis for disease.
BP6 No reputable source classifies NM_198253.2:c.2509C>T as benign.
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 has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 2151563)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.735. BayesDel score = 0.123435.
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; COSV99716414, 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 · 1 PMID not cited in assessment
20301779 ↗ Dyskeratosis Congenita and Related Telomere Biology Disorders. CLINVAR