rs10881982

Variant names:

• chr10-91855239-T-A
• rs10881982
• NM_025235.4:c.2913+113T>A

Your query was ambiguous. Multiple possible variants found:

• chr10-91855239-T-A
• chr10-91855239-T-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_025235.4(TNKS2):​c.2913+113T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0401 in 713,188 control chromosomes in the GnomAD database, including 1,205 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 0.039 (223 hom., cov: 32)
  • Exomes 𝑓: 0.040 (982 hom.)
• Consequence: TNKS2 NM_025235.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 3 publications found

Genes affected

TNKS2 (HGNC:15677): (tankyrase 2) Enables NAD+ ADP-ribosyltransferase activity; enzyme binding activity; and protein ADP-ribosylase activity. Involved in several processes, including protein ADP-ribosylation; protein localization to chromosome, telomeric region; and regulation of telomere maintenance. Located in nuclear envelope; pericentriolar material; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000302365 (HGNC:):

ACMG classification

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 = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNKS2	NM_025235.4	c.2913+113T>A		intron_variant	Intron 22 of 26	ENST00000371627.5	NP_079511.1
TNKS2	XM_011540213.2	c.2976+113T>A		intron_variant	Intron 22 of 26		XP_011538515.1
TNKS2	XM_017016699.2	c.2592+113T>A		intron_variant	Intron 21 of 25		XP_016872188.1
TNKS2	XM_017016700.3	c.1617+113T>A		intron_variant	Intron 10 of 14		XP_016872189.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNKS2	ENST00000371627.5	c.2913+113T>A		intron_variant	Intron 22 of 26	1	NM_025235.4	ENSP00000360689.4

Frequencies

GnomAD3 genomes AF: 0.0390 AC: 5926 AN: 152128 Hom.: 224 Cov.: 32

Gnomad AFR AF: 0.0450

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0278

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.0527

Gnomad FIN AF: 0.0114

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0287

Gnomad OTH AF: 0.0430

GnomAD4 exome AF: 0.0404 AC: 22650 AN: 560942 Hom.: 982 AF XY: 0.0410 AC XY: 12390 AN XY: 302226

African (AFR) AF: 0.0417 AC: 567 AN: 13606

American (AMR) AF: 0.0212 AC: 451 AN: 21242

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 533 AN: 18484

East Asian (EAS) AF: 0.199 AC: 6139 AN: 30858

South Asian (SAS) AF: 0.0485 AC: 2632 AN: 54294

European-Finnish (FIN) AF: 0.0149 AC: 577 AN: 38672

Middle Eastern (MID) AF: 0.0513 AC: 139 AN: 2712

European-Non Finnish (NFE) AF: 0.0295 AC: 10370 AN: 350974

Other (OTH) AF: 0.0413 AC: 1242 AN: 30100

GnomAD4 genome AF: 0.0389 AC: 5923 AN: 152246 Hom.: 223 Cov.: 32 AF XY: 0.0399 AC XY: 2969 AN XY: 74458

African (AFR) AF: 0.0449 AC: 1864 AN: 41522

American (AMR) AF: 0.0277 AC: 424 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3472

East Asian (EAS) AF: 0.206 AC: 1065 AN: 5174

South Asian (SAS) AF: 0.0530 AC: 256 AN: 4832

European-Finnish (FIN) AF: 0.0114 AC: 121 AN: 10610

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0287 AC: 1950 AN: 68020

Other (OTH) AF: 0.0426 AC: 90 AN: 2114

Alfa AF: 0.0310 Hom.: 12

Bravo AF: 0.0412

Asia WGS AF: 0.111 AC: 387 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.043
DANN	Benign	0.18
PhyloP100		-1.9
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

Other links and lift over

dbSNP: rs10881982; hg19: chr10-93614996; COSMIC: COSV107476773;