chr9-69184057-A-G

Position:

• chr9-69184057-A-G

Variant summary

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

The NM_004817.4(TJP2):​c.60+9625A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.905 in 152,242 control chromosomes in the GnomAD database, including 62,440 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 0.91 (62440 hom., cov: 32)
• Consequence: TJP2 NM_004817.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

Genes affected

TJP2 (HGNC:11828): (tight junction protein 2) This gene encodes a zonula occluden that is a member of the membrane-associated guanylate kinase homolog family. The encoded protein functions as a component of the tight junction barrier in epithelial and endothelial cells and is necessary for proper assembly of tight junctions. Mutations in this gene have been identified in patients with hypercholanemia, and genomic duplication of a 270 kb region including this gene causes autosomal dominant deafness-51. Alternatively spliced transcripts encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]

ENSG00000285130 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TJP2	NM_004817.4	c.60+9625A>G		intron_variant		ENST00000377245.9	NP_004808.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TJP2	ENST00000377245.9	c.60+9625A>G		intron_variant		1	NM_004817.4	ENSP00000366453.4
ENSG00000285130	ENST00000642889.1	c.448-28491A>G		intron_variant				ENSP00000493780.1

Frequencies

GnomAD3 genomes AF: 0.905 AC: 137699 AN: 152124 Hom.: 62400 Cov.: 32

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.905 AC: 137795 AN: 152242 Hom.: 62440 Cov.: 32 AF XY: 0.907 AC XY: 67547 AN XY: 74436

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.897

Gnomad4 ASJ AF: 0.924

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.946

Gnomad4 NFE AF: 0.922

Gnomad4 OTH AF: 0.898

Alfa AF: 0.917 Hom.: 38732

Bravo AF: 0.899

Asia WGS AF: 0.904 AC: 3144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3002374; hg19: chr9-71798973;