Variant 3-195868183-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001382273.1(TNK2):c.2115G>A(p.Pro705Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,608,866 control chromosomes in the GnomAD database, including 11,645 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 910 hom., cov: 33)

Exomes 𝑓: 0.12 ( 10735 hom. )

Consequence

TNK2
NM_001382273.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.949

Variant links:

Genes affected

TNK2 (HGNC:19297): (tyrosine kinase non receptor 2) This gene encodes a tyrosine kinase that binds Cdc42Hs in its GTP-bound form and inhibits both the intrinsic and GTPase-activating protein (GAP)-stimulated GTPase activity of Cdc42Hs. This binding is mediated by a unique sequence of 47 amino acids C-terminal to an SH3 domain. The protein may be involved in a regulatory mechanism that sustains the GTP-bound active form of Cdc42Hs and which is directly linked to a tyrosine phosphorylation signal transduction pathway. Several alternatively spliced transcript variants have been identified from this gene, but the full-length nature of only two transcript variants has been determined. [provided by RefSeq, Jul 2008]

TNK2 links:

TNK2 (HGNC:):

TNK2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 3-195868183-C-T is Benign according to our data. Variant chr3-195868183-C-T is described in ClinVar as [Benign]. Clinvar id is 259873.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.949 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNK2	NM_001382273.1 linkuse as main transcript	c.2115G>A	p.Pro705Pro	synonymous_variant	13/16	ENST00000672887.2	NP_001369202.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNK2	ENST00000672887.2 linkuse as main transcript	c.2115G>A	p.Pro705Pro	synonymous_variant	13/16		NM_001382273.1	ENSP00000499899.1		A0A5F9ZGX5

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16065

AN:

151924

Hom.:

911

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.130

Gnomad AMR

AF:

0.0715

Gnomad ASJ

AF:

0.0873

Gnomad EAS

AF:

0.0387

Gnomad SAS

AF:

0.115

Gnomad FIN

AF:

0.0895

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.0988

GnomAD3 exomes

AF:

0.103

AC:

24009

AN:

233702

Hom.:

1403

AF XY:

0.107

AC XY:

13734

AN XY:

128766

show subpopulations

Gnomad AFR exome

AF:

0.105

Gnomad AMR exome

AF:

0.0499

Gnomad ASJ exome

AF:

0.0906

Gnomad EAS exome

AF:

0.0435

Gnomad SAS exome

AF:

0.120

Gnomad FIN exome

AF:

0.0928

Gnomad NFE exome

AF:

0.127

Gnomad OTH exome

AF:

0.109

GnomAD4 exome

AF:

0.118

AC:

172199

AN:

1456824

Hom.:

10735

Cov.:

AF XY:

0.119

AC XY:

86064

AN XY:

724696

show subpopulations

Gnomad4 AFR exome

AF:

0.105

Gnomad4 AMR exome

AF:

0.0531

Gnomad4 ASJ exome

AF:

0.0892

Gnomad4 EAS exome

AF:

0.0537

Gnomad4 SAS exome

AF:

0.124

Gnomad4 FIN exome

AF:

0.0947

Gnomad4 NFE exome

AF:

0.125

Gnomad4 OTH exome

AF:

0.112

GnomAD4 genome

AF:

0.106

AC:

16061

AN:

152042

Hom.:

910

Cov.:

AF XY:

0.104

AC XY:

7693

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.102

Gnomad4 AMR

AF:

0.0714

Gnomad4 ASJ

AF:

0.0873

Gnomad4 EAS

AF:

0.0386

Gnomad4 SAS

AF:

0.115

Gnomad4 FIN

AF:

0.0895

Gnomad4 NFE

AF:

0.123

Gnomad4 OTH

AF:

0.0977

Alfa

AF:

0.117

Hom.:

428

Bravo

AF:

0.104

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.084

DANN

Benign

0.54

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

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