rs176632

chr10-113151320-T-Cchr10-113151320-T-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001367943.1(TCF7L2):c.1001+197T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 152,080 control chromosomes in the GnomAD database, including 60,242 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.89 (60242 hom., cov: 30)
• Consequence: TCF7L2 NM_001367943.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -6.51

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 10-113151320-T-C is Benign according to our data. Variant chr10-113151320-T-C is described in ClinVar as [Benign]. Clinvar id is 1181499.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TCF7L2	NM_001367943.1	c.1001+197T>C		intron_variant		ENST00000355995.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TCF7L2	ENST00000355995.9	c.1001+197T>C		intron_variant		1	NM_001367943.1

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135067 AN: 151962 Hom.: 60194 Cov.: 30

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.947

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.914

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.889 AC: 135172 AN: 152080 Hom.: 60242 Cov.: 30 AF XY: 0.891 AC XY: 66203 AN XY: 74316

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.947

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.895

Gnomad4 FIN AF: 0.854

Gnomad4 NFE AF: 0.850

Gnomad4 OTH AF: 0.910

Alfa AF: 0.868 Hom.: 85130

Bravo AF: 0.900

Asia WGS AF: 0.922 AC: 3208 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.0040
Dann	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs176632; hg19: chr10-114911079;