rs6990300

Variant names:

• chr8-9690351-G-A
• rs6990300
• NM_003747.3:c.1107+9551G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-9690351-G-A
• chr8-9690351-G-C

Variant summary

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

The NM_003747.3(TNKS):​c.1107+9551G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 152,108 control chromosomes in the GnomAD database, including 29,677 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 0.62 (29677 hom., cov: 33)
• Consequence: TNKS NM_003747.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530
• Publications: 8 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.675 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.1107+9551G>A		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.1107+9551G>A		intron	N/A	ENSP00000311579.6	O95271-1
	TNKS	ENST00000517770.2	TSL:4	c.1107+9551G>A		intron	N/A	ENSP00000428185.2	H0YAW5
	TNKS	ENST00000885812.1		c.1107+9551G>A		intron	N/A	ENSP00000555871.1

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94320 AN: 151988 Hom.: 29678 Cov.: 33

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.620 AC: 94343 AN: 152108 Hom.: 29677 Cov.: 33 AF XY: 0.614 AC XY: 45623 AN XY: 74334

African (AFR) AF: 0.551 AC: 22848 AN: 41464

American (AMR) AF: 0.584 AC: 8931 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2710 AN: 3470

East Asian (EAS) AF: 0.478 AC: 2467 AN: 5166

South Asian (SAS) AF: 0.579 AC: 2793 AN: 4822

European-Finnish (FIN) AF: 0.574 AC: 6069 AN: 10578

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.680 AC: 46264 AN: 67996

Other (OTH) AF: 0.659 AC: 1395 AN: 2116

Alfa AF: 0.651 Hom.: 14572

Bravo AF: 0.617

Asia WGS AF: 0.515 AC: 1791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.1
DANN	Benign	0.70
PhyloP100		0.053
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: rs6990300; hg19: chr8-9547861;