chr11-57305759-A-C

Variant names:

• chr11-57305759-A-C
• rs11602501
• NM_033396.3:c.4316+2636T>G

Variant summary

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

The NM_033396.3(TNKS1BP1):​c.4316+2636T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,948 control chromosomes in the GnomAD database, including 22,428 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 0.52 (22428 hom., cov: 31)
• Consequence: TNKS1BP1 NM_033396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 7 publications found

Genes affected

TNKS1BP1 (HGNC:19081): (tankyrase 1 binding protein 1) Enables ankyrin repeat binding activity and enzyme binding activity. Involved in cellular response to ionizing radiation; double-strand break repair; and positive regulation of protein phosphorylation. Located in several cellular components, including actin cytoskeleton; adherens junction; and heterochromatin. Part of CCR4-NOT complex. [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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNKS1BP1	NM_033396.3	c.4316+2636T>G		intron_variant	Intron 6 of 11	ENST00000358252.8	NP_203754.2
TNKS1BP1	XM_006718725.4	c.4316+2636T>G		intron_variant	Intron 6 of 11		XP_006718788.1
TNKS1BP1	XM_011545325.4	c.4316+2636T>G		intron_variant	Intron 6 of 6		XP_011543627.1
TNKS1BP1	XM_047427785.1	c.2288+2636T>G		intron_variant	Intron 2 of 7		XP_047283741.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNKS1BP1	ENST00000358252.8	c.4316+2636T>G		intron_variant	Intron 6 of 11	1	NM_033396.3	ENSP00000350990.3
TNKS1BP1	ENST00000532437.1	c.4316+2636T>G		intron_variant	Intron 5 of 10	1		ENSP00000437271.1
TNKS1BP1	ENST00000528882.5	n.*3102+3132T>G		intron_variant	Intron 6 of 6	5		ENSP00000431616.1

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78443 AN: 151828 Hom.: 22411 Cov.: 31

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.517 AC: 78502 AN: 151948 Hom.: 22428 Cov.: 31 AF XY: 0.507 AC XY: 37632 AN XY: 74254

African (AFR) AF: 0.777 AC: 32166 AN: 41412

American (AMR) AF: 0.389 AC: 5944 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1445 AN: 3468

East Asian (EAS) AF: 0.299 AC: 1542 AN: 5162

South Asian (SAS) AF: 0.351 AC: 1691 AN: 4812

European-Finnish (FIN) AF: 0.365 AC: 3850 AN: 10558

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30281 AN: 67942

Other (OTH) AF: 0.504 AC: 1065 AN: 2112

Alfa AF: 0.467 Hom.: 70483

Bravo AF: 0.530

Asia WGS AF: 0.327 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.58
PhyloP100		-0.38
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: rs11602501; hg19: chr11-57073233;