rs143992655
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_198253.3(TERT):c.1884C>T(p.Asp628Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000198 in 1,613,982 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_198253.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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TERT | NM_198253.3 | c.1884C>T | p.Asp628Asp | synonymous_variant | Exon 4 of 16 | ENST00000310581.10 | NP_937983.2 | |
TERT | NM_001193376.3 | c.1884C>T | p.Asp628Asp | synonymous_variant | Exon 4 of 15 | NP_001180305.1 | ||
TERT | NR_149162.3 | n.1963C>T | non_coding_transcript_exon_variant | Exon 4 of 13 | ||||
TERT | NR_149163.3 | n.1963C>T | non_coding_transcript_exon_variant | Exon 4 of 13 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000880 AC: 134AN: 152260Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.000231 AC: 58AN: 251344Hom.: 0 AF XY: 0.000206 AC XY: 28AN XY: 135906
GnomAD4 exome AF: 0.000127 AC: 186AN: 1461604Hom.: 0 Cov.: 32 AF XY: 0.000111 AC XY: 81AN XY: 727086
GnomAD4 genome AF: 0.000879 AC: 134AN: 152378Hom.: 1 Cov.: 34 AF XY: 0.000859 AC XY: 64AN XY: 74514
ClinVar
Submissions by phenotype
Dyskeratosis congenita Benign:2
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. -
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not specified Benign:1
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Melanoma, cutaneous malignant, susceptibility to, 9 Benign:1
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Idiopathic Pulmonary Fibrosis;C3151443:Dyskeratosis congenita, autosomal dominant 2 Benign:1
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Acute myeloid leukemia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at