8-9715169-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003747.3(TNKS):c.1749+4949A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 151,842 control chromosomes in the GnomAD database, including 26,290 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 0.58 ( 26290 hom., cov: 30)
Consequence
TNKS
NM_003747.3 intron
NM_003747.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.222
Genes affected
TNKS (HGNC:11941): (tankyrase) Enables histone binding activity; pentosyltransferase activity; and zinc ion binding activity. Involved in several processes, including negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric; protein ADP-ribosylation; and regulation of nucleobase-containing compound metabolic process. Acts upstream of or within peptidyl-serine phosphorylation; peptidyl-threonine phosphorylation; and protein ADP-ribosylation. Located in several cellular components, including chromosome, telomeric region; mitotic spindle pole; and nucleus. [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=-0.86).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNKS | NM_003747.3 | c.1749+4949A>G | intron_variant | ENST00000310430.11 | |||
TNKS | XM_011543845.4 | c.1749+4949A>G | intron_variant | ||||
TNKS | XM_011543846.4 | c.1749+4949A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNKS | ENST00000310430.11 | c.1749+4949A>G | intron_variant | 1 | NM_003747.3 | P1 | |||
TNKS | ENST00000517770.2 | c.1749+4949A>G | intron_variant | 4 | |||||
TNKS | ENST00000518281.5 | c.1038+4949A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.584 AC: 88661AN: 151724Hom.: 26287 Cov.: 30
GnomAD3 genomes
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30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.584 AC: 88688AN: 151842Hom.: 26290 Cov.: 30 AF XY: 0.579 AC XY: 42964AN XY: 74198
GnomAD4 genome
?
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88688
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30
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42964
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74198
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1777
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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