chr8-9753028-C-T

Variant names:

• chr8-9753028-C-T
• rs6989782
• NM_003747.3:c.3153+402C>T

Variant summary

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

The NM_003747.3(TNKS):​c.3153+402C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 151,460 control chromosomes in the GnomAD database, including 6,158 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 0.27 (6158 hom., cov: 31)
• Consequence: TNKS NM_003747.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.953

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNKS	NM_003747.3	c.3153+402C>T		intron_variant	Intron 20 of 26	ENST00000310430.11	NP_003738.2
TNKS	XM_011543845.4	c.3153+402C>T		intron_variant	Intron 20 of 27		XP_011542147.1
TNKS	XM_011543846.4	c.3153+402C>T		intron_variant	Intron 20 of 26		XP_011542148.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNKS	ENST00000310430.11	c.3153+402C>T		intron_variant	Intron 20 of 26	1	NM_003747.3	ENSP00000311579.6
TNKS	ENST00000517770.2	c.3153+402C>T		intron_variant	Intron 20 of 27	4		ENSP00000428185.2
TNKS	ENST00000518281.5	c.2442+402C>T		intron_variant	Intron 20 of 26	2		ENSP00000429890.1

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41409 AN: 151356 Hom.: 6160 Cov.: 31

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.273 AC: 41422 AN: 151460 Hom.: 6158 Cov.: 31 AF XY: 0.279 AC XY: 20598 AN XY: 73932

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.250

Alfa AF: 0.282 Hom.: 3033

Bravo AF: 0.271

Asia WGS AF: 0.308 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.37
DANN	Benign	0.71

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: rs6989782; hg19: chr8-9610538; COSMIC: COSV60063686; COSMIC: COSV60063686;