10-101012526-A-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001195263.2(PDZD7):c.1750-268T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 152,052 control chromosomes in the GnomAD database, including 20,749 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.48 ( 20749 hom., cov: 33)
Consequence
PDZD7
NM_001195263.2 intron
NM_001195263.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.237
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 10-101012526-A-C is Benign according to our data. Variant chr10-101012526-A-C is described in ClinVar as [Benign]. Clinvar id is 683852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDZD7 | NM_001195263.2 | c.1750-268T>G | intron_variant | ENST00000619208.6 | NP_001182192.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDZD7 | ENST00000619208.6 | c.1750-268T>G | intron_variant | 5 | NM_001195263.2 | ENSP00000480489 | P1 | |||
PDZD7 | ENST00000644782.1 | c.1523-268T>G | intron_variant | ENSP00000496747 | ||||||
PDZD7 | ENST00000474125.7 | c.*1701-268T>G | intron_variant, NMD_transcript_variant | 2 | ENSP00000474447 |
Frequencies
GnomAD3 genomes AF: 0.482 AC: 73258AN: 151934Hom.: 20753 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.482 AC: 73265AN: 152052Hom.: 20749 Cov.: 33 AF XY: 0.477 AC XY: 35446AN XY: 74298
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 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 | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at