rs763381198
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The ENST00000310581.10(TERT):c.3116C>T(p.Thr1039Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,614,074 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T1039A) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000310581.10 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TERT | NM_198253.3 | c.3116C>T | p.Thr1039Met | missense_variant | 14/16 | ENST00000310581.10 | NP_937983.2 | |
TERT | NM_001193376.3 | c.2927C>T | p.Thr976Met | missense_variant | 13/15 | NP_001180305.1 | ||
TERT | NR_149162.3 | n.2824C>T | non_coding_transcript_exon_variant | 11/13 | ||||
TERT | NR_149163.3 | n.2788C>T | non_coding_transcript_exon_variant | 11/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TERT | ENST00000310581.10 | c.3116C>T | p.Thr1039Met | missense_variant | 14/16 | 1 | NM_198253.3 | ENSP00000309572 | P2 | |
ENST00000666708.1 | n.371G>A | non_coding_transcript_exon_variant | 3/3 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152266Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 248922Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135248
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461808Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 16AN XY: 727196
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74390
ClinVar
Submissions by phenotype
Dyskeratosis congenita Uncertain:1
Uncertain significance, criteria provided, single submitter | curation | Sema4, Sema4 | Jul 16, 2021 | - - |
Idiopathic Pulmonary Fibrosis;C3151443:Dyskeratosis congenita, autosomal dominant 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 12, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at