rs10401120

chr18-55525267-C-T

Variant summary

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

The NM_001083962.2(TCF4):c.145+60013G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 151,768 control chromosomes in the GnomAD database, including 1,828 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 0.11 (1828 hom., cov: 32)
• Consequence: TCF4 NM_001083962.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

Genes affected

TCF4 (HGNC:11634): (transcription factor 4) This gene encodes transcription factor 4, a basic helix-loop-helix transcription factor. The encoded protein recognizes an Ephrussi-box ('E-box') binding site ('CANNTG') - a motif first identified in immunoglobulin enhancers. This gene is broadly expressed, and may play an important role in nervous system development. Defects in this gene are a cause of Pitt-Hopkins syndrome. In addition, an intronic CTG repeat normally numbering 10-37 repeat units can expand to >50 repeat units and cause Fuchs endothelial corneal dystrophy. Multiple alternatively spliced transcript variants that encode different proteins have been described. [provided by RefSeq, Jul 2016]

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 = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TCF4	NM_001083962.2	c.145+60013G>A		intron_variant		ENST00000354452.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TCF4	ENST00000354452.8	c.145+60013G>A		intron_variant		5	NM_001083962.2	P3

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17261 AN: 151662 Hom.: 1822 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0526

Gnomad FIN AF: 0.0450

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0436

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.114 AC: 17304 AN: 151768 Hom.: 1828 Cov.: 32 AF XY: 0.112 AC XY: 8303 AN XY: 74162

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.0726

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0533

Gnomad4 FIN AF: 0.0450

Gnomad4 NFE AF: 0.0436

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0690 Hom.: 586

Bravo AF: 0.123

Asia WGS AF: 0.0470 AC: 166 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	3.5
Dann	Benign	0.54

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: rs10401120; hg19: chr18-53192498;