5-1280191-G-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_198253.3(TERT):c.1917C>A(p.Val639Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,613,972 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TERT | NM_198253.3 | c.1917C>A | p.Val639Val | synonymous_variant | Exon 4 of 16 | ENST00000310581.10 | NP_937983.2 | |
TERT | NM_001193376.3 | c.1917C>A | p.Val639Val | synonymous_variant | Exon 4 of 15 | NP_001180305.1 | ||
TERT | NR_149162.3 | n.1996C>A | non_coding_transcript_exon_variant | Exon 4 of 13 | ||||
TERT | NR_149163.3 | n.1996C>A | non_coding_transcript_exon_variant | Exon 4 of 13 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152242Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000955 AC: 24AN: 251368Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135886
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461730Hom.: 0 Cov.: 32 AF XY: 0.0000261 AC XY: 19AN XY: 727158
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152242Hom.: 0 Cov.: 34 AF XY: 0.0000538 AC XY: 4AN XY: 74380
ClinVar
Submissions by phenotype
Idiopathic Pulmonary Fibrosis;C3151443:Dyskeratosis congenita, autosomal dominant 2 Benign:1
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Dyskeratosis congenita Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at