rs61018535

Positions:

• chr6-43481492-C-A
• chr6-43481492-C-G
• chr6-43481492-C-T

Variant summary

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

The NM_001350562.2(TJAP1):​c.-122+3260C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 136,816 control chromosomes in the GnomAD database, including 2,827 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 0.13 (2827 hom., cov: 26)
• Consequence: TJAP1 NM_001350562.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

TJAP1 (HGNC:17949): (tight junction associated protein 1) This gene encodes a tight junction-associated protein. Incorporation of the encoded protein into tight junctions occurs at a late stage of formation of the junctions. The encoded protein localizes to the Golgi and may function in vesicle trafficking. Alternatively spliced transcript variants have been described. A related pseudogene exists on the X chromosome. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TJAP1	NM_001350562.2	c.-122+3260C>A		intron_variant		ENST00000372449.6	NP_001337491.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TJAP1	ENST00000372449.6	c.-122+3260C>A		intron_variant		5	NM_001350562.2	ENSP00000361527	A1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 18261 AN: 136728 Hom.: 2818 Cov.: 26

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.0672

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.0430

Gnomad SAS AF: 0.0904

Gnomad FIN AF: 0.0332

Gnomad MID AF: 0.0616

Gnomad NFE AF: 0.0286

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.134 AC: 18301 AN: 136816 Hom.: 2827 Cov.: 26 AF XY: 0.134 AC XY: 8798 AN XY: 65842

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.0672

Gnomad4 ASJ AF: 0.0496

Gnomad4 EAS AF: 0.0431

Gnomad4 SAS AF: 0.0899

Gnomad4 FIN AF: 0.0332

Gnomad4 NFE AF: 0.0286

Gnomad4 OTH AF: 0.110

Alfa AF: 0.00799 Hom.: 2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.24
DANN	Benign	0.045

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: rs61018535; hg19: chr6-43449230;