chr5-1253629-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_198253.3(TERT):c.*99C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 998,776 control chromosomes in the GnomAD database, including 16,193 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_198253.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TERT | NM_198253.3 | c.*99C>T | 3_prime_UTR_variant | Exon 16 of 16 | ENST00000310581.10 | NP_937983.2 | ||
TERT | NM_001193376.3 | c.*99C>T | 3_prime_UTR_variant | Exon 15 of 15 | NP_001180305.1 | |||
TERT | NR_149162.3 | n.3206C>T | non_coding_transcript_exon_variant | Exon 13 of 13 | ||||
TERT | NR_149163.3 | n.3170C>T | non_coding_transcript_exon_variant | Exon 13 of 13 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.193 AC: 29371AN: 152112Hom.: 3357 Cov.: 33
GnomAD4 exome AF: 0.162 AC: 137406AN: 846546Hom.: 12833 Cov.: 11 AF XY: 0.158 AC XY: 69096AN XY: 437754
GnomAD4 genome AF: 0.193 AC: 29409AN: 152230Hom.: 3360 Cov.: 33 AF XY: 0.186 AC XY: 13858AN XY: 74432
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 22% of patients studied by a panel of primary immunodeficiencies. Number of patients: 21. Only high quality variants are reported. -
Aplastic anemia Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Dyskeratosis congenita, autosomal dominant 2 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 1 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at