rs61018535

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.15
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 UniProt
TJAP1NM_001350562.2 linkuse as main transcriptc.-122+3260C>A intron_variant ENST00000372449.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TJAP1ENST00000372449.6 linkuse as main transcriptc.-122+3260C>A intron_variant 5 NM_001350562.2 A1Q5JTD0-1

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs61018535; hg19: chr6-43449230; API