Variant chr10-112950403-TC-T 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.-345del variant causes a 5 prime UTR change. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.50 ( 18348 hom., cov: 0)

Exomes 𝑓: 0.31 ( 4378 hom. )

Consequence

TCF7L2
NM_001367943.1 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.67

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 10-112950403-TC-T is Benign according to our data. Variant chr10-112950403-TC-T is described in ClinVar as [Benign]. Clinvar id is 1276639.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.531 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.-345del		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.-345del		5_prime_UTR_variant	1/15	1	NM_001367943.1	ENSP00000348274		Q9NQB0-1

Frequencies

GnomAD3 genomes

AF:

0.503

AC:

70142

AN:

139412

Hom.:

18336

Cov.:

show subpopulations

Gnomad AFR

AF:

0.538

Gnomad AMI

AF:

0.603

Gnomad AMR

AF:

0.501

Gnomad ASJ

AF:

0.541

Gnomad EAS

AF:

0.0622

Gnomad SAS

AF:

0.361

Gnomad FIN

AF:

0.424

Gnomad MID

AF:

0.537

Gnomad NFE

AF:

0.530

Gnomad OTH

AF:

0.529

GnomAD4 exome

AF:

0.305

AC:

16897

AN:

55320

Hom.:

4378

Cov.:

AF XY:

0.299

AC XY:

8127

AN XY:

27192

show subpopulations

Gnomad4 AFR exome

AF:

0.420

Gnomad4 AMR exome

AF:

0.283

Gnomad4 ASJ exome

AF:

0.433

Gnomad4 EAS exome

AF:

0.0476

Gnomad4 SAS exome

AF:

0.136

Gnomad4 FIN exome

AF:

0.138

Gnomad4 NFE exome

AF:

0.380

Gnomad4 OTH exome

AF:

0.362

GnomAD4 genome

AF:

0.503

AC:

70158

AN:

139436

Hom.:

18348

Cov.:

AF XY:

0.494

AC XY:

33118

AN XY:

67052

show subpopulations

Gnomad4 AFR

AF:

0.537

Gnomad4 AMR

AF:

0.501

Gnomad4 ASJ

AF:

0.541

Gnomad4 EAS

AF:

0.0624

Gnomad4 SAS

AF:

0.362

Gnomad4 FIN

AF:

0.424

Gnomad4 NFE

AF:

0.530

Gnomad4 OTH

AF:

0.527

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 15, 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