rs17747324

chr10-112992744-T-Cchr10-112992744-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367943.1(TCF7L2):c.450+28120T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 151,562 control chromosomes in the GnomAD database, including 2,794 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 0.17 (2794 hom., cov: 31)
• Consequence: TCF7L2 NM_001367943.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TCF7L2	NM_001367943.1	c.450+28120T>C		intron_variant		ENST00000355995.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TCF7L2	ENST00000355995.9	c.450+28120T>C		intron_variant		1	NM_001367943.1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26353 AN: 151448 Hom.: 2790 Cov.: 31

Gnomad AFR AF: 0.0657

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.0185

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.174 AC: 26367 AN: 151562 Hom.: 2794 Cov.: 31 AF XY: 0.172 AC XY: 12751 AN XY: 74072

Gnomad4 AFR AF: 0.0659

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.0186

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.224

Alfa AF: 0.193 Hom.: 723

Bravo AF: 0.167

Asia WGS AF: 0.104 AC: 365 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.1
Dann	Benign	0.52

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

Other links and lift over

dbSNP: rs17747324; hg19: chr10-114752503;