5-1293617-G-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_198253.3(TERT):c.1269C>A(p.Ala423=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,550,082 control chromosomes in the GnomAD database, including 2 homozygotes. 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. A423A) has been classified as Likely benign.
Frequency
Consequence
NM_198253.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TERT | NM_198253.3 | c.1269C>A | p.Ala423= | synonymous_variant | 2/16 | ENST00000310581.10 | |
TERT | NM_001193376.3 | c.1269C>A | p.Ala423= | synonymous_variant | 2/15 | ||
TERT | NR_149162.3 | n.1348C>A | non_coding_transcript_exon_variant | 2/13 | |||
TERT | NR_149163.3 | n.1348C>A | non_coding_transcript_exon_variant | 2/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TERT | ENST00000310581.10 | c.1269C>A | p.Ala423= | synonymous_variant | 2/16 | 1 | NM_198253.3 | P2 | |
TERT | ENST00000334602.10 | c.1269C>A | p.Ala423= | synonymous_variant | 2/15 | 1 | A2 | ||
TERT | ENST00000460137.6 | c.1269C>A | p.Ala423= | synonymous_variant, NMD_transcript_variant | 2/13 | 1 | |||
TERT | ENST00000656021.1 | c.1269C>A | p.Ala423= | synonymous_variant, NMD_transcript_variant | 2/17 |
Frequencies
GnomAD3 genomes ? AF: 0.000539 AC: 82AN: 152228Hom.: 2 Cov.: 34
GnomAD3 exomes AF: 0.000125 AC: 19AN: 152406Hom.: 0 AF XY: 0.0000612 AC XY: 5AN XY: 81656
GnomAD4 exome AF: 0.0000572 AC: 80AN: 1397736Hom.: 0 Cov.: 32 AF XY: 0.0000406 AC XY: 28AN XY: 688948
GnomAD4 genome ? AF: 0.000538 AC: 82AN: 152346Hom.: 2 Cov.: 34 AF XY: 0.000524 AC XY: 39AN XY: 74498
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 10, 2016 | - - |
Idiopathic Pulmonary Fibrosis;C3151443:Dyskeratosis congenita, autosomal dominant 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | TERT: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at