5-1293424-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 4P and 3B. PM1PM2BP4_ModerateBP6
The NM_198253.3(TERT):c.1462C>T(p.Leu488Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,524 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_198253.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TERT | NM_198253.3 | c.1462C>T | p.Leu488Phe | missense_variant | 2/16 | ENST00000310581.10 | |
TERT | NM_001193376.3 | c.1462C>T | p.Leu488Phe | missense_variant | 2/15 | ||
TERT | NR_149162.3 | n.1541C>T | non_coding_transcript_exon_variant | 2/13 | |||
TERT | NR_149163.3 | n.1541C>T | non_coding_transcript_exon_variant | 2/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TERT | ENST00000310581.10 | c.1462C>T | p.Leu488Phe | missense_variant | 2/16 | 1 | NM_198253.3 | P2 | |
TERT | ENST00000334602.10 | c.1462C>T | p.Leu488Phe | missense_variant | 2/15 | 1 | A2 | ||
TERT | ENST00000460137.6 | c.1462C>T | p.Leu488Phe | missense_variant, NMD_transcript_variant | 2/13 | 1 | |||
TERT | ENST00000656021.1 | c.1462C>T | p.Leu488Phe | missense_variant, NMD_transcript_variant | 2/17 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.00000805 AC: 2AN: 248298Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134888
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460524Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726558
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 30, 2016 | - - |
Idiopathic Pulmonary Fibrosis;C3151443:Dyskeratosis congenita, autosomal dominant 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 16, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at