chr1-61864462-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001350145.3(PATJ):c.2664G>A(p.Leu888=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00985 in 1,613,954 control chromosomes in the GnomAD database, including 105 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0079 ( 6 hom., cov: 32)
Exomes 𝑓: 0.010 ( 99 hom. )
Consequence
PATJ
NM_001350145.3 synonymous
NM_001350145.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0800
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 1-61864462-G-A is Benign according to our data. Variant chr1-61864462-G-A is described in ClinVar as [Benign]. Clinvar id is 779063.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.08 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 6 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PATJ | NM_001350145.3 | c.2664G>A | p.Leu888= | synonymous_variant | 20/44 | ENST00000642238.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PATJ | ENST00000642238.2 | c.2664G>A | p.Leu888= | synonymous_variant | 20/44 | NM_001350145.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00794 AC: 1209AN: 152192Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.00777 AC: 1954AN: 251418Hom.: 20 AF XY: 0.00771 AC XY: 1047AN XY: 135880
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GnomAD4 exome AF: 0.0100 AC: 14684AN: 1461644Hom.: 99 Cov.: 33 AF XY: 0.00965 AC XY: 7018AN XY: 727150
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GnomAD4 genome ? AF: 0.00793 AC: 1208AN: 152310Hom.: 6 Cov.: 32 AF XY: 0.00779 AC XY: 580AN XY: 74472
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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 | Invitae | Mar 02, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at