rs5002815

Variant names:

• chr8-9609661-G-T
• rs5002815
• NM_003747.3:c.899-5921G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003747.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNKS	NM_003747.3	MANE Select	c.899-5921G>T		intron	N/A	NP_003738.2	O95271-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNKS	ENST00000310430.11	TSL:1 MANE Select	c.899-5921G>T		intron	N/A	ENSP00000311579.6	O95271-1
	TNKS	ENST00000517770.2	TSL:4	c.899-5921G>T		intron	N/A	ENSP00000428185.2	H0YAW5
	TNKS	ENST00000885812.1		c.899-5921G>T		intron	N/A	ENSP00000555871.1

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

African (AFR) AF: 0.189 AC: 7855 AN: 41458

American (AMR) AF: 0.111 AC: 1700 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0695 AC: 241 AN: 3468

East Asian (EAS) AF: 0.0942 AC: 488 AN: 5180

South Asian (SAS) AF: 0.181 AC: 871 AN: 4818

European-Finnish (FIN) AF: 0.0817 AC: 863 AN: 10564

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0746 AC: 5068 AN: 67972

Other (OTH) AF: 0.107 AC: 226 AN: 2110

Alfa AF: 0.0858 Hom.: 1041

Bravo AF: 0.117

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.5
DANN	Benign	0.78
PhyloP100		0.064
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5002815; hg19: chr8-9467171;