rs5002815

chr8-9609661-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003747.3(TNKS):c.899-5921G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,064 control chromosomes in the GnomAD database, including 1,156 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 0.11 (1156 hom., cov: 32)
• Consequence: TNKS NM_003747.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNKS	NM_003747.3	c.899-5921G>T		intron_variant		ENST00000310430.11
TNKS	XM_011543845.4	c.899-5921G>T		intron_variant
TNKS	XM_011543846.4	c.899-5921G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNKS	ENST00000310430.11	c.899-5921G>T		intron_variant		1	NM_003747.3	P1
TNKS	ENST00000517770.2	c.899-5921G>T		intron_variant		4
TNKS	ENST00000518281.5	c.188-5921G>T		intron_variant		2
TNKS	ENST00000520408.5	c.899-5921G>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17298 AN: 151946 Hom.: 1147 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0695

Gnomad EAS AF: 0.0942

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0746

Gnomad OTH AF: 0.103

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.114 AC: 17342 AN: 152064 Hom.: 1156 Cov.: 32 AF XY: 0.116 AC XY: 8618 AN XY: 74334

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0695

Gnomad4 EAS AF: 0.0942

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.0817

Gnomad4 NFE AF: 0.0746

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0815 Hom.: 635

Bravo AF: 0.117

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.5
Dann	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5002815; hg19: chr8-9467171;