chr6-43481492-C-A

Variant names:

• chr6-43481492-C-A
• rs61018535
• NM_001350562.2:c.-122+3260C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001350562.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TJAP1	NM_001350562.2	MANE Select	c.-122+3260C>A		intron	N/A	NP_001337491.1
	TJAP1	NM_001146016.2		c.-125+3260C>A		intron	N/A	NP_001139488.1
	TJAP1	NM_001350561.2		c.-177+2774C>A		intron	N/A	NP_001337490.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TJAP1	ENST00000372449.6	TSL:5 MANE Select	c.-122+3260C>A		intron	N/A	ENSP00000361527.1
	TJAP1	ENST00000372445.9	TSL:1	c.-125+3260C>A		intron	N/A	ENSP00000361522.5
	TJAP1	ENST00000871118.1		c.-122+3864C>A		intron	N/A	ENSP00000541177.1

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

African (AFR) AF: 0.375 AC: 14381 AN: 38376

American (AMR) AF: 0.0672 AC: 917 AN: 13646

Ashkenazi Jewish (ASJ) AF: 0.0496 AC: 162 AN: 3264

East Asian (EAS) AF: 0.0431 AC: 203 AN: 4710

South Asian (SAS) AF: 0.0899 AC: 367 AN: 4082

European-Finnish (FIN) AF: 0.0332 AC: 263 AN: 7932

Middle Eastern (MID) AF: 0.0667 AC: 18 AN: 270

European-Non Finnish (NFE) AF: 0.0286 AC: 1766 AN: 61782

Other (OTH) AF: 0.110 AC: 209 AN: 1904

Alfa AF: 0.0663 Hom.: 247

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.24
DANN	Benign	0.045
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs61018535; hg19: chr6-43449230;