Variant 11-57302651-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The ENST00000358252.8(TNKS1BP1):c.4491G>A(p.Leu1497Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00145 in 1,610,430 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0018 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0014 ( 25 hom. )

Consequence

TNKS1BP1
ENST00000358252.8 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.356

Variant links:

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]

TNKS1BP1 links:

TNKS1BP1 (HGNC:):

TNKS1BP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 11-57302651-C-T is Benign according to our data. Variant chr11-57302651-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2641791.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.356 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNKS1BP1	NM_033396.3 linkuse as main transcript	c.4491G>A	p.Leu1497Leu	synonymous_variant	7/12	ENST00000358252.8	NP_203754.2	Q9C0C2-1A0A024R542
TNKS1BP1	XM_006718725.4 linkuse as main transcript	c.4491G>A	p.Leu1497Leu	synonymous_variant	7/12		XP_006718788.1	Q9C0C2-1A0A024R542
TNKS1BP1	XM_047427785.1 linkuse as main transcript	c.2463G>A	p.Leu821Leu	synonymous_variant	3/8		XP_047283741.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TNKS1BP1	ENST00000358252.8 linkuse as main transcript	c.4491G>A	p.Leu1497Leu	synonymous_variant	7/12	1	NM_033396.3	ENSP00000350990.3	Q9C0C2-1
TNKS1BP1	ENST00000532437.1 linkuse as main transcript	c.4491G>A	p.Leu1497Leu	synonymous_variant	6/11	1		ENSP00000437271.1	Q9C0C2-1
TNKS1BP1	ENST00000528882.5 linkuse as main transcript	n.*3103-2690G>A		intron_variant		5		ENSP00000431616.1	E9PKK0
TNKS1BP1	ENST00000427750.2 linkuse as main transcript	n.829G>A		non_coding_transcript_exon_variant	1/6	2

Frequencies

GnomAD3 genomes

AF:

0.00179

AC:

273

AN:

152134

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00106

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00183

Gnomad ASJ

AF:

0.0352

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0000941

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.000956

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00239

AC:

586

AN:

245312

Hom.:

AF XY:

0.00219

AC XY:

291

AN XY:

132980

show subpopulations

Gnomad AFR exome

AF:

0.00146

Gnomad AMR exome

AF:

0.00300

Gnomad ASJ exome

AF:

0.0280

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000167

Gnomad FIN exome

AF:

0.0000512

Gnomad NFE exome

AF:

0.00121

Gnomad OTH exome

AF:

0.00685

GnomAD4 exome

AF:

0.00142

AC:

2065

AN:

1458178

Hom.:

Cov.:

AF XY:

0.00144

AC XY:

1041

AN XY:

725324

show subpopulations

Gnomad4 AFR exome

AF:

0.00185

Gnomad4 AMR exome

AF:

0.00291

Gnomad4 ASJ exome

AF:

0.0303

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000303

Gnomad4 FIN exome

AF:

0.0000972

Gnomad4 NFE exome

AF:

0.000689

Gnomad4 OTH exome

AF:

0.00383

GnomAD4 genome

AF:

0.00179

AC:

273

AN:

152252

Hom.:

Cov.:

AF XY:

0.00168

AC XY:

125

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.00106

Gnomad4 AMR

AF:

0.00183

Gnomad4 ASJ

AF:

0.0352

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0000941

Gnomad4 NFE

AF:

0.000956

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00379

Hom.:

Bravo

AF:

0.00216

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00158

EpiControl

AF:

0.00208

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

TNKS1BP1: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.96

DANN

Benign

0.52

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over