Variant 10-112950449-G-GT details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001367943.1(TCF7L2):c.-294dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.21 ( 2955 hom., cov: 17)

Exomes 𝑓: 0.16 ( 30 hom. )

Consequence

TCF7L2
NM_001367943.1 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.385

Variant links:

Genes affected

TCF7L2 (HGNC:11641): (transcription factor 7 like 2) This gene encodes a high mobility group (HMG) box-containing transcription factor that plays a key role in the Wnt signaling pathway. The protein has been implicated in blood glucose homeostasis. Genetic variants of this gene are associated with increased risk of type 2 diabetes. Several transcript variants encoding multiple different isoforms have been found for this gene.[provided by RefSeq, Oct 2010]

TCF7L2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 10-112950449-G-GT is Benign according to our data. Variant chr10-112950449-G-GT is described in ClinVar as [Benign]. Clinvar id is 1274713.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TCF7L2	NM_001367943.1 linkuse as main transcript	c.-294dup		5_prime_UTR_variant	1/15	ENST00000355995.9	NP_001354872.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TCF7L2	ENST00000355995.9 linkuse as main transcript	c.-294dup		5_prime_UTR_variant	1/15	1	NM_001367943.1	ENSP00000348274		Q9NQB0-1

Frequencies

GnomAD3 genomes

AF:

0.208

AC:

25078

AN:

120542

Hom.:

2953

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0881

Gnomad AMI

AF:

0.382

Gnomad AMR

AF:

0.240

Gnomad ASJ

AF:

0.247

Gnomad EAS

AF:

0.0498

Gnomad SAS

AF:

0.160

Gnomad FIN

AF:

0.144

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.283

Gnomad OTH

AF:

0.226

GnomAD4 exome

AF:

0.157

AC:

11337

AN:

72310

Hom.:

Cov.:

AF XY:

0.153

AC XY:

5536

AN XY:

36170

show subpopulations

Gnomad4 AFR exome

AF:

0.112

Gnomad4 AMR exome

AF:

0.156

Gnomad4 ASJ exome

AF:

0.190

Gnomad4 EAS exome

AF:

0.0906

Gnomad4 SAS exome

AF:

0.0878

Gnomad4 FIN exome

AF:

0.0694

Gnomad4 NFE exome

AF:

0.179

Gnomad4 OTH exome

AF:

0.173

GnomAD4 genome

AF:

0.208

AC:

25078

AN:

120552

Hom.:

2955

Cov.:

AF XY:

0.200

AC XY:

11394

AN XY:

56886

show subpopulations

Gnomad4 AFR

AF:

0.0880

Gnomad4 AMR

AF:

0.240

Gnomad4 ASJ

AF:

0.247

Gnomad4 EAS

AF:

0.0497

Gnomad4 SAS

AF:

0.160

Gnomad4 FIN

AF:

0.144

Gnomad4 NFE

AF:

0.283

Gnomad4 OTH

AF:

0.225

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 19, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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