rs10903314

Positions:

• chr8-9609596-C-T

Variant summary

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

The NM_003747.3(TNKS):​c.899-5986C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 151,980 control chromosomes in the GnomAD database, including 6,589 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 0.29 (6589 hom., cov: 32)
• Consequence: TNKS NM_003747.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNKS	NM_003747.3	c.899-5986C>T		intron_variant		ENST00000310430.11	NP_003738.2
TNKS	XM_011543845.4	c.899-5986C>T		intron_variant			XP_011542147.1
TNKS	XM_011543846.4	c.899-5986C>T		intron_variant			XP_011542148.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNKS	ENST00000310430.11	c.899-5986C>T		intron_variant		1	NM_003747.3	ENSP00000311579	P1
TNKS	ENST00000517770.2	c.899-5986C>T		intron_variant		4		ENSP00000428185
TNKS	ENST00000518281.5	c.188-5986C>T		intron_variant		2		ENSP00000429890
TNKS	ENST00000520408.5	c.899-5986C>T		intron_variant		2		ENSP00000428299

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43677 AN: 151862 Hom.: 6567 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.288 AC: 43741 AN: 151980 Hom.: 6589 Cov.: 32 AF XY: 0.292 AC XY: 21708 AN XY: 74286

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.247

Alfa AF: 0.257 Hom.: 2475

Bravo AF: 0.280

Asia WGS AF: 0.361 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.0
DANN	Benign	0.75

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: rs10903314; hg19: chr8-9467106;