14-20377362-A-C
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_007110.5(TEP1):āc.6006T>Gā(p.Leu2002=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0646 in 1,614,060 control chromosomes in the GnomAD database, including 3,636 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.065 ( 375 hom., cov: 32)
Exomes š: 0.065 ( 3261 hom. )
Consequence
TEP1
NM_007110.5 synonymous
NM_007110.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.271
Genes affected
TEP1 (HGNC:11726): (telomerase associated protein 1) This gene product is a component of the ribonucleoprotein complex responsible for telomerase activity which catalyzes the addition of new telomeres on the chromosome ends. The telomerase-associated proteins are conserved from ciliates to humans. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP7
Synonymous conserved (PhyloP=-0.271 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.087 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TEP1 | NM_007110.5 | c.6006T>G | p.Leu2002= | synonymous_variant | 41/55 | ENST00000262715.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEP1 | ENST00000262715.10 | c.6006T>G | p.Leu2002= | synonymous_variant | 41/55 | 1 | NM_007110.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0649 AC: 9870AN: 152156Hom.: 374 Cov.: 32
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GnomAD3 exomes AF: 0.0597 AC: 15006AN: 251364Hom.: 584 AF XY: 0.0628 AC XY: 8534AN XY: 135874
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GnomAD4 exome AF: 0.0645 AC: 94329AN: 1461786Hom.: 3261 Cov.: 33 AF XY: 0.0656 AC XY: 47737AN XY: 727204
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GnomAD4 genome AF: 0.0649 AC: 9877AN: 152274Hom.: 375 Cov.: 32 AF XY: 0.0650 AC XY: 4842AN XY: 74450
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Not reported inComputational scores
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Benign
CADD
Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at