rs41515848

chr18-55242588-G-A

Variant summary

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

The NM_001083962.2(TCF4):c.1351-7905C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0804 in 151,654 control chromosomes in the GnomAD database, including 608 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 0.080 (608 hom., cov: 32)
• Consequence: TCF4 NM_001083962.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TCF4	NM_001083962.2	c.1351-7905C>T		intron_variant		ENST00000354452.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TCF4	ENST00000354452.8	c.1351-7905C>T		intron_variant		5	NM_001083962.2	P3

Frequencies

GnomAD3 genomes AF: 0.0804 AC: 12180 AN: 151556 Hom.: 609 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.0644

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.00348

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0284

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0652

Gnomad OTH AF: 0.0842

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

GnomAD4 genome AF: 0.0804 AC: 12186 AN: 151654 Hom.: 608 Cov.: 32 AF XY: 0.0785 AC XY: 5814 AN XY: 74070

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.0643

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.00349

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0284

Gnomad4 NFE AF: 0.0652

Gnomad4 OTH AF: 0.0840

Alfa AF: 0.0708 Hom.: 146

Bravo AF: 0.0837

Asia WGS AF: 0.0550 AC: 194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.13
Dann	Benign	0.51

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: rs41515848; hg19: chr18-52909819;