rs2228026
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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.1719T>Cā(p.Ile573=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0499 in 1,613,912 control chromosomes in the GnomAD database, including 2,297 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 0.038 ( 153 hom., cov: 32)
Exomes š: 0.051 ( 2144 hom. )
Consequence
TEP1
NM_007110.5 synonymous
NM_007110.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0740
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=-0.82).
BP7
Synonymous conserved (PhyloP=-0.074 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0806 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TEP1 | NM_007110.5 | c.1719T>C | p.Ile573= | synonymous_variant | 11/55 | ENST00000262715.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEP1 | ENST00000262715.10 | c.1719T>C | p.Ile573= | synonymous_variant | 11/55 | 1 | NM_007110.5 | P1 | |
TEP1 | ENST00000556935.5 | c.1395T>C | p.Ile465= | synonymous_variant | 9/53 | 1 | |||
TEP1 | ENST00000555727.5 | c.1719T>C | p.Ile573= | synonymous_variant, NMD_transcript_variant | 11/54 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0385 AC: 5856AN: 152128Hom.: 153 Cov.: 32
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GnomAD3 exomes AF: 0.0473 AC: 11898AN: 251412Hom.: 406 AF XY: 0.0517 AC XY: 7018AN XY: 135876
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GnomAD4 exome AF: 0.0511 AC: 74626AN: 1461666Hom.: 2144 Cov.: 31 AF XY: 0.0528 AC XY: 38363AN XY: 727146
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GnomAD4 genome AF: 0.0385 AC: 5855AN: 152246Hom.: 153 Cov.: 32 AF XY: 0.0403 AC XY: 3000AN XY: 74444
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at