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GeneBe

9-27123262-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000459.5(TEK):c.52+13620A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 151,556 control chromosomes in the GnomAD database, including 2,986 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 0.18 ( 2986 hom., cov: 30)

Consequence

TEK
NM_000459.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.880
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TEKNM_000459.5 linkuse as main transcriptc.52+13620A>G intron_variant ENST00000380036.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TEKENST00000380036.10 linkuse as main transcriptc.52+13620A>G intron_variant 1 NM_000459.5 P1Q02763-1

Frequencies

GnomAD3 genomes
AF:
0.176
AC:
26660
AN:
151440
Hom.:
2980
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.156
Gnomad AMI
AF:
0.116
Gnomad AMR
AF:
0.144
Gnomad ASJ
AF:
0.0912
Gnomad EAS
AF:
0.530
Gnomad SAS
AF:
0.461
Gnomad FIN
AF:
0.213
Gnomad MID
AF:
0.196
Gnomad NFE
AF:
0.148
Gnomad OTH
AF:
0.157
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.176
AC:
26676
AN:
151556
Hom.:
2986
Cov.:
30
AF XY:
0.184
AC XY:
13643
AN XY:
74016
show subpopulations
Gnomad4 AFR
AF:
0.156
Gnomad4 AMR
AF:
0.144
Gnomad4 ASJ
AF:
0.0912
Gnomad4 EAS
AF:
0.530
Gnomad4 SAS
AF:
0.461
Gnomad4 FIN
AF:
0.213
Gnomad4 NFE
AF:
0.148
Gnomad4 OTH
AF:
0.161
Alfa
AF:
0.151
Hom.:
4329
Bravo
AF:
0.165
Asia WGS
AF:
0.452
AC:
1567
AN:
3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
2.6
Dann
Benign
0.57

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.

Other links and lift over

dbSNP: rs603085; hg19: chr9-27123260; API