rs10514164
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_001114394.3(TENT2):āc.1086T>Gā(p.Pro362=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0196 in 1,612,488 control chromosomes in the GnomAD database, including 1,585 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 0.028 ( 218 hom., cov: 31)
Exomes š: 0.019 ( 1367 hom. )
Consequence
TENT2
NM_001114394.3 synonymous
NM_001114394.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.40
Genes affected
TENT2 (HGNC:26776): (terminal nucleotidyltransferase 2) Enables 5'-3' RNA polymerase activity and polynucleotide adenylyltransferase activity. Involved in RNA metabolic process and negative regulation of RNA catabolic process. Predicted to be located in nucleus. Predicted to be part of nuclear RNA-directed RNA polymerase complex. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP7
?
Synonymous conserved (PhyloP=3.4 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TENT2 | NM_001114394.3 | c.1086T>G | p.Pro362= | synonymous_variant | 12/15 | ENST00000453514.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENT2 | ENST00000453514.6 | c.1086T>G | p.Pro362= | synonymous_variant | 12/15 | 5 | NM_001114394.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0278 AC: 4223AN: 152178Hom.: 218 Cov.: 31
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GnomAD3 exomes AF: 0.0449 AC: 11266AN: 250882Hom.: 1065 AF XY: 0.0384 AC XY: 5204AN XY: 135646
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GnomAD4 exome AF: 0.0187 AC: 27307AN: 1460192Hom.: 1367 Cov.: 31 AF XY: 0.0184 AC XY: 13375AN XY: 726392
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GnomAD4 genome ? AF: 0.0278 AC: 4237AN: 152296Hom.: 218 Cov.: 31 AF XY: 0.0306 AC XY: 2280AN XY: 74480
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ClinVar
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