Variant chr9-27109315-T-TG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_000459.5(TEK):c.-275dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 571,032 control chromosomes in the GnomAD database, including 10,134 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.11 ( 1794 hom., cov: 31)

Exomes 𝑓: 0.11 ( 8340 hom. )

Consequence

TEK
NM_000459.5 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.81

Variant links:

Genes affected

TEK (HGNC:11724): (TEK receptor tyrosine kinase) This gene encodes a receptor that belongs to the protein tyrosine kinase Tie2 family. The encoded protein possesses a unique extracellular region that contains two immunoglobulin-like domains, three epidermal growth factor (EGF)-like domains and three fibronectin type III repeats. The ligand angiopoietin-1 binds to this receptor and mediates a signaling pathway that functions in embryonic vascular development. Mutations in this gene are associated with inherited venous malformations of the skin and mucous membranes. Alternative splicing results in multiple transcript variants. Additional alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Feb 2014]

TEK links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 9-27109315-T-TG is Benign according to our data. Variant chr9-27109315-T-TG is described in ClinVar as [Benign]. Clinvar id is 366388.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
TEK	NM_000459.5 linkuse as main transcript	c.-275dup	5_prime_UTR_variant	1/23	ENST00000380036.10
TEK	NM_001290077.1 linkuse as main transcript	c.-275dup	5_prime_UTR_variant	1/22
TEK	NM_001290078.1 linkuse as main transcript	c.-275dup	5_prime_UTR_variant	1/21

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEK	ENST00000380036.10 linkuse as main transcript	c.-275dup	5_prime_UTR_variant	1/23	1	NM_000459.5	P1	Q02763-1
TEK	ENST00000519097.5 linkuse as main transcript	c.-275dup	5_prime_UTR_variant	1/21	2			Q02763-3
TEK	ENST00000615002.4 linkuse as main transcript	c.-275dup	5_prime_UTR_variant	1/23	5

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15960

AN:

152060

Hom.:

1782

Cov.:

show subpopulations

Gnomad AFR

AF:

0.120

Gnomad AMI

AF:

0.0241

Gnomad AMR

AF:

0.159

Gnomad ASJ

AF:

0.0214

Gnomad EAS

AF:

0.615

Gnomad SAS

AF:

0.190

Gnomad FIN

AF:

0.104

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0449

Gnomad OTH

AF:

0.0880

GnomAD4 exome

AF:

0.113

AC:

47298

AN:

418854

Hom.:

8340

Cov.:

AF XY:

0.114

AC XY:

24887

AN XY:

218788

show subpopulations

Gnomad4 AFR exome

AF:

0.122

Gnomad4 AMR exome

AF:

0.192

Gnomad4 ASJ exome

AF:

0.0196

Gnomad4 EAS exome

AF:

0.668

Gnomad4 SAS exome

AF:

0.157

Gnomad4 FIN exome

AF:

0.0969

Gnomad4 NFE exome

AF:

0.0454

Gnomad4 OTH exome

AF:

0.0984

GnomAD4 genome

AF:

0.105

AC:

15997

AN:

152178

Hom.:

1794

Cov.:

AF XY:

0.113

AC XY:

8433

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.120

Gnomad4 AMR

AF:

0.160

Gnomad4 ASJ

AF:

0.0214

Gnomad4 EAS

AF:

0.615

Gnomad4 SAS

AF:

0.190

Gnomad4 FIN

AF:

0.104

Gnomad4 NFE

AF:

0.0449

Gnomad4 OTH

AF:

0.0946

Alfa

AF:

0.0686

Hom.:

Bravo

AF:

0.113

Asia WGS

AF:

0.358

AC:

1241

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Multiple cutaneous and mucosal venous malformations

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

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