rs1334806555
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The ENST00000310581.10(TERT):c.892T>A(p.Ser298Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000317 in 1,575,906 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. S298C) 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.892T>A | p.Ser298Thr | missense_variant | 2/16 | ENST00000310581.10 | NP_937983.2 | |
TERT | NM_001193376.3 | c.892T>A | p.Ser298Thr | missense_variant | 2/15 | NP_001180305.1 | ||
TERT | NR_149162.3 | n.971T>A | non_coding_transcript_exon_variant | 2/13 | ||||
TERT | NR_149163.3 | n.971T>A | non_coding_transcript_exon_variant | 2/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TERT | ENST00000310581.10 | c.892T>A | p.Ser298Thr | missense_variant | 2/16 | 1 | NM_198253.3 | ENSP00000309572 | P2 | |
TERT | ENST00000334602.10 | c.892T>A | p.Ser298Thr | missense_variant | 2/15 | 1 | ENSP00000334346 | A2 | ||
TERT | ENST00000460137.6 | c.892T>A | p.Ser298Thr | missense_variant, NMD_transcript_variant | 2/13 | 1 | ENSP00000425003 | |||
TERT | ENST00000656021.1 | c.892T>A | p.Ser298Thr | missense_variant, NMD_transcript_variant | 2/17 | ENSP00000499759 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000106 AC: 2AN: 187918Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 102002
GnomAD4 exome AF: 0.00000281 AC: 4AN: 1423742Hom.: 0 Cov.: 35 AF XY: 0.00000283 AC XY: 2AN XY: 705708
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74340
ClinVar
Submissions by phenotype
Dyskeratosis congenita Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 31, 2022 | The p.S298T variant (also known as c.892T>A), located in coding exon 2 of the TERT gene, results from a T to A substitution at nucleotide position 892. The serine at codon 298 is replaced by threonine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Idiopathic Pulmonary Fibrosis;C3151443:Dyskeratosis congenita, autosomal dominant 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at