rs554739019
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_198253.3(TERT):c.3165G>T(p.Ser1055=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,620 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S1055S) has been classified as Likely benign.
Frequency
Consequence
NM_198253.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TERT | NM_198253.3 | c.3165G>T | p.Ser1055= | synonymous_variant | 15/16 | ENST00000310581.10 | |
TERT | NM_001193376.3 | c.2976G>T | p.Ser992= | synonymous_variant | 14/15 | ||
TERT | NR_149162.3 | n.2873G>T | non_coding_transcript_exon_variant | 12/13 | |||
TERT | NR_149163.3 | n.2837G>T | non_coding_transcript_exon_variant | 12/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TERT | ENST00000310581.10 | c.3165G>T | p.Ser1055= | synonymous_variant | 15/16 | 1 | NM_198253.3 | P2 | |
ENST00000666708.1 | n.289-176C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000410 AC: 1AN: 243746Hom.: 0 AF XY: 0.00000750 AC XY: 1AN XY: 133352
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459620Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726106
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Dyskeratosis congenita Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 17, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at