10-113127459-A-G

Position:

• chr10-113127459-A-G

Variant summary

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

The NM_001367943.1(TCF7L2):​c.553-13725A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,150 control chromosomes in the GnomAD database, including 37,779 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 0.69 (37779 hom., cov: 33)
• Consequence: TCF7L2 NM_001367943.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TCF7L2	NM_001367943.1	c.553-13725A>G		intron_variant		ENST00000355995.9	NP_001354872.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TCF7L2	ENST00000355995.9	c.553-13725A>G		intron_variant		1	NM_001367943.1	ENSP00000348274

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104879 AN: 152032 Hom.: 37734 Cov.: 33

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.690 AC: 104975 AN: 152150 Hom.: 37779 Cov.: 33 AF XY: 0.686 AC XY: 51004 AN XY: 74398

Gnomad4 AFR AF: 0.888

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.677

Alfa AF: 0.639 Hom.: 9761

Bravo AF: 0.703

Asia WGS AF: 0.464 AC: 1619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.65

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: rs7906315; hg19: chr10-114887218;