rs150917752
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001195263.2(PDZD7):c.156C>T(p.Asn52=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000808 in 1,608,340 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00080 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00081 ( 11 hom. )
Consequence
PDZD7
NM_001195263.2 synonymous
NM_001195263.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.364
Genes affected
PDZD7 (HGNC:26257): (PDZ domain containing 7) This gene encodes a ciliary protein homologous to proteins which are mutated in Usher syndrome patients, and mutations and translocations involving this gene have been associated with two types of Usher syndrome. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
Variant 10-101030064-G-A is Benign according to our data. Variant chr10-101030064-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 46208.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-101030064-G-A is described in Lovd as [Benign]. Variant chr10-101030064-G-A is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=0.364 with no splicing effect.
BS1
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.000809 (1178/1456692) while in subpopulation EAS AF= 0.0124 (488/39380). AF 95% confidence interval is 0.0115. There are 11 homozygotes in gnomad4_exome. There are 628 alleles in male gnomad4_exome subpopulation. Median coverage is 35. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 11 AR,Digenic gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDZD7 | NM_001195263.2 | c.156C>T | p.Asn52= | synonymous_variant | 2/17 | ENST00000619208.6 | NP_001182192.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDZD7 | ENST00000619208.6 | c.156C>T | p.Asn52= | synonymous_variant | 2/17 | 5 | NM_001195263.2 | ENSP00000480489 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000792 AC: 120AN: 151520Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00132 AC: 332AN: 250814Hom.: 3 AF XY: 0.00133 AC XY: 181AN XY: 135738
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GnomAD4 exome AF: 0.000809 AC: 1178AN: 1456692Hom.: 11 Cov.: 35 AF XY: 0.000867 AC XY: 628AN XY: 724716
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GnomAD4 genome AF: 0.000798 AC: 121AN: 151648Hom.: 0 Cov.: 33 AF XY: 0.00112 AC XY: 83AN XY: 74154
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:5
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | PDZD7: BP4, BP7, BS2 - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 08, 2023 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 30, 2012 | Asn52Asn in Exon 02 of PDZD7: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and has been identified in 3/7020 European Americ an chromosomes from a broad population by the NHLBI Exome Sequencing Project (ht tp://evs.gs.washington.edu/EVS; dbSNP rs150917752). - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at