rs1538833
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_025235.4(TNKS2):c.2060-323G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0942 in 152,182 control chromosomes in the GnomAD database, including 766 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: 𝑓 0.094 ( 766 hom., cov: 32)
Consequence
TNKS2
NM_025235.4 intron
NM_025235.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.00200
Genes affected
TNKS2 (HGNC:15677): (tankyrase 2) Enables NAD+ ADP-ribosyltransferase activity; enzyme binding activity; and protein ADP-ribosylase activity. Involved in several processes, including protein ADP-ribosylation; protein localization to chromosome, telomeric region; and regulation of telomere maintenance. Located in nuclear envelope; pericentriolar material; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNKS2 | NM_025235.4 | c.2060-323G>A | intron_variant | ENST00000371627.5 | |||
TNKS2 | XM_011540213.2 | c.2123-323G>A | intron_variant | ||||
TNKS2 | XM_017016699.2 | c.1739-323G>A | intron_variant | ||||
TNKS2 | XM_017016700.3 | c.764-323G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNKS2 | ENST00000371627.5 | c.2060-323G>A | intron_variant | 1 | NM_025235.4 | P1 | |||
TNKS2 | ENST00000710380.1 | c.2099-323G>A | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0942 AC: 14326AN: 152064Hom.: 762 Cov.: 32
GnomAD3 genomes
?
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14326
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0942 AC: 14334AN: 152182Hom.: 766 Cov.: 32 AF XY: 0.0970 AC XY: 7219AN XY: 74394
GnomAD4 genome
?
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14334
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152182
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32
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7219
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74394
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528
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at