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TERT
Final classification
VUS
TERT c.899G>A · p.Gly300Asp
TERT

NM_198253.2:c.899G>A (p.Gly300Asp) is a rare missense variant in TERT that is absent from population databases, with 0 alleles observed across 1,571,010 alleles in gnomAD v4.1, meeting PM2 (moderate) criterion.

Gene
TERT
Transcript
NM_198253.2
HGVS · transcript:coding
NM_198253.2:c.899G>A
Consequence
N/A
GRCh38
chr5:1293987 C>T
GRCh37
chr5:1294102 C>T
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; combination = 1 moderate, 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; combination = 1 moderate, which maps to VUS.
Classification rationale
PM2 VUS
TERT c.899G>A

NM_198253.2:c.899G>A (p.Gly300Asp) is a rare missense variant in TERT that is absent from population databases, with 0 alleles observed across 1,571,010 alleles in gnomAD v4.1, meeting PM2 (moderate) criterion.1 This variant has been reported in ClinVar as Uncertain Significance by a single clinical laboratory (Variation ID 2937435; Labcorp Genetics). The classification is based on 1-star review status and does not meet the 3-star expert panel threshold for PP5 or BP6.2 In silico predictors are inconclusive: REVEL (0.283) is intermediate, BayesDel (-0.187) is marginally in the benign direction, and SpliceAI predicts no splicing impact (max delta 0.00). No consensus supports either pathogenicity (PP3) or benignity (BP4).3 No functional studies (PS3/BS3), case-control data (PS4), de novo observations (PS2/PM6), co-segregation data (PP1/BS4), or same-residue pathogenic comparators (PM5/PS1) are available for this variant.4 The variant is a missense substitution and does not qualify for PVS1 null-variant assessment.5 Based on the available evidence, this variant meets only one moderate pathogenicity criterion (PM2). Under the ACMG/AMP 2015 scoring framework, this alone is insufficient to classify the variant as Likely Pathogenic or Pathogenic. The variant remains a Variant of Uncertain Significance.6

PM2 VUS
3 revelbayesdelspliceai ↗
4 oncokb ↗pm5_candidatespvs1_variant_assessment
5 pvs1_generic_framework ↗pvs1_variant_assessment
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 moderate Pathogenic
NM_198253.2:c.899G>A is absent from population databases. In gnomAD v4.1, the variant has 0 alleles across 1,571,010 total alleles (AF=0.00%), meeting the PM2 threshold for absence in population controls (AF < 0.1%).
gnomAD v2.1: absentgnomAD v4.1: 0/1571
Assessed · not applied
Pathogenic
PS1 No evidence that the same amino acid change (p.Gly300Asp) resulting from a different nucleotide substitution has been previously established as pathogenic.
PS2 No de novo observation data for NM_198253.2:c.899G>A was identified.
PS3 No variant-specific functional data exists for NM_198253.2:c.899G>A (p.Gly300Asp).
PS4 No case-control or cohort data demonstrating statistically significant enrichment of NM_198253.2:c.899G>A in affected individuals compared to controls.
PM1 Position p.Gly300 is not located in a statistically significant mutational hotspot (cancerhotspots.org).
PM5 No pathogenic missense variant at the same amino acid residue (p.Gly300) was identified in ClinVar.
PM6 No de novo observation for NM_198253.2:c.899G>A was identified in ClinVar submissions or published literature.
PP1 No co-segregation data is available for NM_198253.2:c.899G>A.
PP2 PP2 requires demonstration that the gene has a low rate of benign missense variation and that missense variants are a common mechanism of disease.
PP3 In silico predictors do not provide multiple lines of supporting evidence for pathogenicity.
PP4 No patient phenotype or family history data is available for the proband carrying NM_198253.2:c.899G>A.
PP5 ClinVar reports NM_198253.2:c.899G>A as Uncertain Significance (1 star, criteria provided by a single submitter).
Benign
BA1 NM_198253.2:c.899G>A is absent from gnomAD (0/1,571,010 alleles).
BS1 NM_198253.2:c.899G>A is absent from gnomAD (0/1,571,010 alleles).
BS2 No homozygous observations of NM_198253.2:c.899G>A in gnomAD or other population databases.
BS3 No well-established functional studies demonstrate a neutral effect for NM_198253.2:c.899G>A (p.Gly300Asp).
BS4 No segregation data is available for NM_198253.2:c.899G>A.
BP1 BP1 applies to missense variants in genes where primarily truncating variants are known to cause disease.
BP2 No evidence that NM_198253.2:c.899G>A has been observed in trans with a known pathogenic variant in TERT for a recessive disorder.
BP4 In silico predictors do not provide multiple lines of evidence suggesting no impact.
BP5 No evidence that NM_198253.2:c.899G>A has been observed in a case with an alternate molecular basis for disease.
BP6 ClinVar reports NM_198253.2:c.899G>A as Uncertain Significance, not benign.
N/A · 3 PVS1 · BP3 · 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= 0; MAF= 0.00000%, 0/1571010 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/73820 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
Absent · 0 / 1,571,010
0 hom
Not observed in any ancestry group.
+ 10 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, 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 (1 clinical laboratory). (ClinVarID = 2937435)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.283. BayesDel score = -0.187223.
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 not previously been reported in somatic cancers (COSMIC).
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