chr8-9743407-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003747.3(TNKS):c.2644-4617T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,192 control chromosomes in the GnomAD database, including 3,146 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 0.18 ( 3146 hom., cov: 32)
Exomes 𝑓: 0.25 ( 0 hom. )
Consequence
TNKS
NM_003747.3 intron
NM_003747.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.914
Publications
8 publications found
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 was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNKS | NM_003747.3 | c.2644-4617T>C | intron_variant | Intron 17 of 26 | ENST00000310430.11 | NP_003738.2 | ||
TNKS | XM_011543845.4 | c.2644-4617T>C | intron_variant | Intron 17 of 27 | XP_011542147.1 | |||
TNKS | XM_011543846.4 | c.2644-4617T>C | intron_variant | Intron 17 of 26 | XP_011542148.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.178 AC: 27054AN: 152068Hom.: 3137 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
27054
AN:
152068
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.250 AC: 1AN: 4Hom.: 0 AF XY: 0.250 AC XY: 1AN XY: 4 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
4
Hom.:
AF XY:
AC XY:
1
AN XY:
4
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
1
AN:
4
Other (OTH)
AC:
0
AN:
0
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.178 AC: 27076AN: 152188Hom.: 3146 Cov.: 32 AF XY: 0.181 AC XY: 13458AN XY: 74392 show subpopulations
GnomAD4 genome
AF:
AC:
27076
AN:
152188
Hom.:
Cov.:
32
AF XY:
AC XY:
13458
AN XY:
74392
show subpopulations
African (AFR)
AF:
AC:
1846
AN:
41558
American (AMR)
AF:
AC:
3804
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
AC:
610
AN:
3470
East Asian (EAS)
AF:
AC:
2254
AN:
5154
South Asian (SAS)
AF:
AC:
1466
AN:
4828
European-Finnish (FIN)
AF:
AC:
1902
AN:
10594
Middle Eastern (MID)
AF:
AC:
54
AN:
294
European-Non Finnish (NFE)
AF:
AC:
14415
AN:
67978
Other (OTH)
AF:
AC:
397
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1067
2135
3202
4270
5337
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
304
608
912
1216
1520
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1154
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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