10-101010570-A-G
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001195263.2(PDZD7):āc.2319T>Cā(p.Arg773=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 1,515,998 control chromosomes in the GnomAD database, including 518,457 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. RSRSR773R) has been classified as Likely benign.
Frequency
Consequence
NM_001195263.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDZD7 | NM_001195263.2 | c.2319T>C | p.Arg773= | synonymous_variant | 15/17 | ENST00000619208.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZD7 | ENST00000619208.6 | c.2319T>C | p.Arg773= | synonymous_variant | 15/17 | 5 | NM_001195263.2 | P1 | |
PDZD7 | ENST00000474125.7 | c.*2266T>C | 3_prime_UTR_variant, NMD_transcript_variant | 11/13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.815 AC: 123470AN: 151424Hom.: 50309 Cov.: 30
GnomAD3 exomes AF: 0.808 AC: 102589AN: 127004Hom.: 41568 AF XY: 0.807 AC XY: 55472AN XY: 68772
GnomAD4 exome AF: 0.829 AC: 1131112AN: 1364456Hom.: 468101 Cov.: 92 AF XY: 0.827 AC XY: 555077AN XY: 670886
GnomAD4 genome AF: 0.815 AC: 123570AN: 151542Hom.: 50356 Cov.: 30 AF XY: 0.813 AC XY: 60233AN XY: 74086
ClinVar
Submissions by phenotype
not specified Benign:5
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 30, 2012 | Arg773Arg in Exon 15 of PDZD7: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and has been identified in 26.3% (31/118) of chr omosomes from a population in the dbSNP database (http://www.ncbi.nlm.nih.gov/pr ojects/SNP; rs807022). - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 02, 2014 | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 02, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Usher syndrome type 2C Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Hearing loss, autosomal recessive 57 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at