rs4915789
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001350145.3(PATJ):c.3493-135A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 450,278 control chromosomes in the GnomAD database, including 99,729 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 0.64 ( 31577 hom., cov: 31)
Exomes 𝑓: 0.67 ( 68152 hom. )
Consequence
PATJ
NM_001350145.3 intron
NM_001350145.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.834
Genes affected
PATJ (HGNC:28881): (PATJ crumbs cell polarity complex component) This gene encodes a protein with multiple PDZ domains. PDZ domains mediate protein-protein interactions, and proteins with multiple PDZ domains often organize multimeric complexes at the plasma membrane. This protein localizes to tight junctions and to the apical membrane of epithelial cells. A similar protein in Drosophila is a scaffolding protein which tethers several members of a multimeric signaling complex in photoreceptors. [provided by RefSeq, Jul 2008]
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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=-0.92).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PATJ | NM_001350145.3 | c.3493-135A>G | intron_variant | ENST00000642238.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PATJ | ENST00000642238.2 | c.3493-135A>G | intron_variant | NM_001350145.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.642 AC: 97475AN: 151844Hom.: 31550 Cov.: 31
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GnomAD4 exome AF: 0.671 AC: 200244AN: 298318Hom.: 68152 AF XY: 0.676 AC XY: 108210AN XY: 159996
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GnomAD4 genome ? AF: 0.642 AC: 97555AN: 151960Hom.: 31577 Cov.: 31 AF XY: 0.649 AC XY: 48180AN XY: 74274
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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