18-55586153-GAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGC-GAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGC

Variant names:

• chr18-55586153-G-GAGCAGCAGC
• rs55725917
• NM_001083962.2:c.73-810_73-802dupGCTGCTGCT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_001083962.2(TCF4):​c.73-810_73-802dupGCTGCTGCT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0096 (40 hom., cov: 0)
  • Exomes 𝑓: 0.012 (460 hom.)
• Consequence: TCF4 NM_001083962.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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 -8 ACMG points.

• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0096 (1301/135494) while in subpopulation EAS AF= 0.0253 (111/4380). AF 95% confidence interval is 0.0215. There are 40 homozygotes in gnomad4. There are 670 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 1301 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCF4	NM_001083962.2	c.73-810_73-802dupGCTGCTGCT		intron_variant	Intron 2 of 19	ENST00000354452.8	NP_001077431.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCF4	ENST00000354452.8	c.73-810_73-802dupGCTGCTGCT		intron_variant	Intron 2 of 19	5	NM_001083962.2	ENSP00000346440.3

Frequencies

GnomAD3 genomes AF: 0.00960 AC: 1300 AN: 135404 Hom.: 39 Cov.: 0

Gnomad AFR AF: 0.00650

Gnomad AMI AF: 0.0156

Gnomad AMR AF: 0.00603

Gnomad ASJ AF: 0.00850

Gnomad EAS AF: 0.0253

Gnomad SAS AF: 0.0206

Gnomad FIN AF: 0.0205

Gnomad MID AF: 0.0197

Gnomad NFE AF: 0.00877

Gnomad OTH AF: 0.00808

GnomAD4 exome AF: 0.0120 AC: 6837 AN: 571604 Hom.: 460 Cov.: 0 AF XY: 0.0125 AC XY: 3746 AN XY: 298616

Gnomad4 AFR exome AF: 0.00583

Gnomad4 AMR exome AF: 0.00500

Gnomad4 ASJ exome AF: 0.00989

Gnomad4 EAS exome AF: 0.0470

Gnomad4 SAS exome AF: 0.0204

Gnomad4 FIN exome AF: 0.0367

Gnomad4 NFE exome AF: 0.00774

Gnomad4 OTH exome AF: 0.0136

GnomAD4 genome AF: 0.00960 AC: 1301 AN: 135494 Hom.: 40 Cov.: 0 AF XY: 0.0102 AC XY: 670 AN XY: 65518

Gnomad4 AFR AF: 0.00648

Gnomad4 AMR AF: 0.00603

Gnomad4 ASJ AF: 0.00850

Gnomad4 EAS AF: 0.0253

Gnomad4 SAS AF: 0.0211

Gnomad4 FIN AF: 0.0205

Gnomad4 NFE AF: 0.00875

Gnomad4 OTH AF: 0.00800

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs55725917; hg19: chr18-53253384;