chr1-61861632-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001350145.3(PATJ):c.2404G>C(p.Asp802His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00211 in 1,471,416 control chromosomes in the GnomAD database, including 65 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.012 ( 39 hom., cov: 30)
Exomes 𝑓: 0.0010 ( 26 hom. )
Consequence
PATJ
NM_001350145.3 missense
NM_001350145.3 missense
Scores
1
11
Clinical Significance
Conservation
PhyloP100: 2.06
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.002489537).
BP6
?
Variant 1-61861632-G-C is Benign according to our data. Variant chr1-61861632-G-C is described in ClinVar as [Benign]. Clinvar id is 775134.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0115 (1754/152108) while in subpopulation AFR AF= 0.0403 (1670/41484). AF 95% confidence interval is 0.0386. There are 39 homozygotes in gnomad4. There are 821 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 39 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PATJ | NM_001350145.3 | c.2404G>C | p.Asp802His | missense_variant | 19/44 | ENST00000642238.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PATJ | ENST00000642238.2 | c.2404G>C | p.Asp802His | missense_variant | 19/44 | NM_001350145.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0115 AC: 1751AN: 151990Hom.: 39 Cov.: 30
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GnomAD3 exomes AF: 0.00291 AC: 534AN: 183542Hom.: 12 AF XY: 0.00215 AC XY: 219AN XY: 101676
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GnomAD4 exome AF: 0.00103 AC: 1355AN: 1319308Hom.: 26 Cov.: 22 AF XY: 0.000950 AC XY: 625AN XY: 658176
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GnomAD4 genome ? AF: 0.0115 AC: 1754AN: 152108Hom.: 39 Cov.: 30 AF XY: 0.0110 AC XY: 821AN XY: 74368
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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 | May 31, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N
PrimateAI
Benign
T
Polyphen
0.76
.;.;P;.
Vest4
0.25, 0.18
MVP
0.56
MPC
0.48
ClinPred
T
GERP RS
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gMVP
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