chr9-69174188-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1
The NM_201629.3(TJP2):c.-185G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 1,382,578 control chromosomes in the GnomAD database, including 27,460 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.17 ( 2258 hom., cov: 33)
Exomes 𝑓: 0.20 ( 25202 hom. )
Consequence
TJP2
NM_201629.3 5_prime_UTR
NM_201629.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.727
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
?
Variant 9-69174188-G-A is Benign according to our data. Variant chr9-69174188-G-A is described in ClinVar as [Benign]. Clinvar id is 1251404.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TJP2 | NM_201629.3 | c.-185G>A | 5_prime_UTR_variant | 1/21 | |||
TJP2 | XM_047424092.1 | c.-341G>A | 5_prime_UTR_variant | 1/24 | |||
TJP2 | NM_001170414.2 | c.-10+22417G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TJP2 | ENST00000423935.6 | c.-10+22417G>A | intron_variant | 2 | |||||
TJP2 | ENST00000606364.5 | c.-10+22417G>A | intron_variant | 4 | |||||
TJP2 | ENST00000636438.1 | c.237+22417G>A | intron_variant | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.167 AC: 25434AN: 151854Hom.: 2258 Cov.: 33
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GnomAD4 exome AF: 0.198 AC: 243261AN: 1230616Hom.: 25202 Cov.: 38 AF XY: 0.197 AC XY: 117281AN XY: 594276
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 06, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at