rs11145465
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000636438.1(TJP2):c.143C>A(p.Ser48Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.204 in 1,231,738 control chromosomes in the GnomAD database, including 26,683 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 0.19 ( 2736 hom., cov: 31)
Exomes 𝑓: 0.21 ( 23947 hom. )
Consequence
TJP2
ENST00000636438.1 missense
ENST00000636438.1 missense
Scores
1
5
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.46
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]
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 (MetaRNN=0.0018132925).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TJP2 | NM_001170414.2 | c.-104C>A | 5_prime_UTR_variant | 2/22 | |||
TJP2 | NM_001369870.1 | c.-104C>A | 5_prime_UTR_variant | 2/24 | |||
TJP2 | NM_001369871.1 | c.-222C>A | 5_prime_UTR_variant | 2/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TJP2 | ENST00000636438.1 | c.143C>A | p.Ser48Tyr | missense_variant | 2/24 | 5 | A2 | ||
TJP2 | ENST00000423935.6 | c.-104C>A | 5_prime_UTR_variant | 2/6 | 2 | ||||
TJP2 | ENST00000606364.5 | c.-104C>A | 5_prime_UTR_variant | 2/6 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.187 AC: 28403AN: 151866Hom.: 2736 Cov.: 31
GnomAD3 genomes
?
AF:
AC:
28403
AN:
151866
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.206 AC: 222643AN: 1079754Hom.: 23947 Cov.: 31 AF XY: 0.207 AC XY: 105263AN XY: 509744
GnomAD4 exome
AF:
AC:
222643
AN:
1079754
Hom.:
Cov.:
31
AF XY:
AC XY:
105263
AN XY:
509744
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.187 AC: 28408AN: 151984Hom.: 2736 Cov.: 31 AF XY: 0.184 AC XY: 13650AN XY: 74284
GnomAD4 genome
?
AF:
AC:
28408
AN:
151984
Hom.:
Cov.:
31
AF XY:
AC XY:
13650
AN XY:
74284
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
841
ALSPAC
AF:
AC:
805
Asia WGS
AF:
AC:
214
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MutationTaster
Benign
P;P
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at