rs10885399

Variant names:

• chr10-112966418-T-A
• rs10885399
• NM_001367943.1:c.450+1794T>A

Your query was ambiguous. Multiple possible variants found:

• chr10-112966418-T-A
• chr10-112966418-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367943.1(TCF7L2):​c.450+1794T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 151,078 control chromosomes in the GnomAD database, including 12,625 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 0.36 (12625 hom., cov: 30)
• Consequence: TCF7L2 NM_001367943.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452
• Publications: 8 publications found

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 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• neurodevelopmental disorder

  Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
• intellectual disability

  Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
• congenital glaucoma

  Inheritance: Unknown Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367943.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCF7L2	NM_001367943.1	MANE Select	c.450+1794T>A		intron	N/A	NP_001354872.1
	TCF7L2	NM_001146274.2		c.450+1794T>A		intron	N/A	NP_001139746.1
	TCF7L2	NM_030756.5		c.381+14811T>A		intron	N/A	NP_110383.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCF7L2	ENST00000355995.9	TSL:1 MANE Select	c.450+1794T>A		intron	N/A	ENSP00000348274.4
	TCF7L2	ENST00000627217.3	TSL:1	c.450+1794T>A		intron	N/A	ENSP00000486891.1
	TCF7L2	ENST00000369397.8	TSL:1	c.381+14811T>A		intron	N/A	ENSP00000358404.4

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53580 AN: 150956 Hom.: 12574 Cov.: 30

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.355 AC: 53681 AN: 151078 Hom.: 12625 Cov.: 30 AF XY: 0.353 AC XY: 26096 AN XY: 73834

African (AFR) AF: 0.644 AC: 26291 AN: 40818

American (AMR) AF: 0.265 AC: 4023 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1218 AN: 3462

East Asian (EAS) AF: 0.678 AC: 3488 AN: 5144

South Asian (SAS) AF: 0.360 AC: 1721 AN: 4776

European-Finnish (FIN) AF: 0.187 AC: 1964 AN: 10512

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13964 AN: 67876

Other (OTH) AF: 0.338 AC: 713 AN: 2108

Alfa AF: 0.112 Hom.: 167

Bravo AF: 0.379

Asia WGS AF: 0.511 AC: 1778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.83
PhyloP100		0.45
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10885399; hg19: chr10-114726177;