chr5-1294893-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_198253.3(TERT):c.97C>T(p.Pro33Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000156 in 1,282,832 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely risk allele (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P33L) has been classified as Uncertain significance.
Frequency
Consequence
NM_198253.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TERT | NM_198253.3 | c.97C>T | p.Pro33Ser | missense_variant | 1/16 | ENST00000310581.10 | |
TERT | NM_001193376.3 | c.97C>T | p.Pro33Ser | missense_variant | 1/15 | ||
TERT | NR_149162.3 | n.176C>T | non_coding_transcript_exon_variant | 1/13 | |||
TERT | NR_149163.3 | n.176C>T | non_coding_transcript_exon_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TERT | ENST00000310581.10 | c.97C>T | p.Pro33Ser | missense_variant | 1/16 | 1 | NM_198253.3 | P2 | |
TERT | ENST00000334602.10 | c.97C>T | p.Pro33Ser | missense_variant | 1/15 | 1 | A2 | ||
TERT | ENST00000460137.6 | c.97C>T | p.Pro33Ser | missense_variant, NMD_transcript_variant | 1/13 | 1 | |||
TERT | ENST00000656021.1 | c.97C>T | p.Pro33Ser | missense_variant, NMD_transcript_variant | 1/17 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome AF: 0.00000156 AC: 2AN: 1282832Hom.: 0 Cov.: 34 AF XY: 0.00000158 AC XY: 1AN XY: 630968
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
Pulmonary fibrosis Pathogenic:1
Likely risk allele, no assertion criteria provided | research | Garcia Pulmonary Genetics Research Laboratory, Columbia University Irving Medical Center | Jun 09, 2022 | Leukocyte telomere length (by qPCR) less than 10th percentile age-adjusted - |
Interstitial lung disease 2 Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at