5-1264542-T-C
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_198253.3(TERT):c.2705A>G(p.Lys902Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K902N) has been classified as Pathogenic.
Frequency
Consequence
NM_198253.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TERT | NM_198253.3 | c.2705A>G | p.Lys902Arg | missense_variant | 11/16 | ENST00000310581.10 | |
TERT | NM_001193376.3 | c.2654+1922A>G | intron_variant | ||||
TERT | NR_149162.3 | n.2551+1922A>G | intron_variant, non_coding_transcript_variant | ||||
TERT | NR_149163.3 | n.2515+1922A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TERT | ENST00000310581.10 | c.2705A>G | p.Lys902Arg | missense_variant | 11/16 | 1 | NM_198253.3 | P2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 26, 2011 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at