rs397516632
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004817.4(TJP2):c.2880+72G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000629 in 1,510,906 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000055 ( 0 hom. )
Consequence
TJP2
NM_004817.4 intron
NM_004817.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0210
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 9-69248296-G-A is Benign according to our data. Variant chr9-69248296-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 44108.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-69248296-G-A is described in Lovd as [Likely_benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TJP2 | NM_004817.4 | c.2880+72G>A | intron_variant | ENST00000377245.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TJP2 | ENST00000377245.9 | c.2880+72G>A | intron_variant | 1 | NM_004817.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152208Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000882 AC: 11AN: 124648Hom.: 0 AF XY: 0.000125 AC XY: 8AN XY: 63924
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GnomAD4 exome AF: 0.0000552 AC: 75AN: 1358580Hom.: 0 Cov.: 32 AF XY: 0.0000587 AC XY: 39AN XY: 664886
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GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152326Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74492
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 18, 2013 | p.Val984Val in TJP2: This variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located within the sp lice consensus sequence. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at