NM_003747.3:c.3447+259G>A

Variant names:

• chr8-9765049-G-A
• rs6986755
• NM_003747.3:c.3447+259G>A

Variant summary

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

The NM_003747.3(TNKS):​c.3447+259G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,146 control chromosomes in the GnomAD database, including 1,301 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 (1301 hom., cov: 32)
• Consequence: TNKS NM_003747.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.82
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNKS	NM_003747.3	c.3447+259G>A		intron_variant	Intron 23 of 26	ENST00000310430.11	NP_003738.2
TNKS	XM_011543845.4	c.3447+259G>A		intron_variant	Intron 23 of 27		XP_011542147.1
TNKS	XM_011543846.4	c.3447+259G>A		intron_variant	Intron 23 of 26		XP_011542148.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNKS	ENST00000310430.11	c.3447+259G>A		intron_variant	Intron 23 of 26	1	NM_003747.3	ENSP00000311579.6
TNKS	ENST00000517770.2	c.3447+259G>A		intron_variant	Intron 23 of 27	4		ENSP00000428185.2
TNKS	ENST00000518281.5	c.2736+259G>A		intron_variant	Intron 23 of 26	2		ENSP00000429890.1

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16992 AN: 152028 Hom.: 1290 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0782

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0658

Gnomad OTH AF: 0.0937

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

GnomAD4 genome AF: 0.112 AC: 17040 AN: 152146 Hom.: 1301 Cov.: 32 AF XY: 0.113 AC XY: 8395 AN XY: 74380

African (AFR) AF: 0.208 AC: 8645 AN: 41498

American (AMR) AF: 0.0861 AC: 1317 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0579 AC: 201 AN: 3470

East Asian (EAS) AF: 0.104 AC: 540 AN: 5178

South Asian (SAS) AF: 0.166 AC: 798 AN: 4816

European-Finnish (FIN) AF: 0.0782 AC: 828 AN: 10582

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0658 AC: 4477 AN: 68002

Other (OTH) AF: 0.0974 AC: 205 AN: 2104

Alfa AF: 0.0796 Hom.: 1058

Bravo AF: 0.114

Asia WGS AF: 0.163 AC: 567 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	0.017
DANN	Benign	0.56
PhyloP100		-2.8
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: rs6986755; hg19: chr8-9622559;