rs200896335
Positions:
- chr10-101010536-TGCTGCGGCTGCG-T
- chr10-101010536-TGCTGCGGCTGCG-TGCTGCG
- chr10-101010536-TGCTGCGGCTGCG-TGCTGCGGCTGCGGCTGCG
- chr10-101010536-TGCTGCGGCTGCG-TGCTGCGGCTGCGGCTGCGGCTGCGGCTACGGCTGCGGCTGCGGCTGCG
- chr10-101010536-TGCTGCGGCTGCG-TGCTGCGGCTGCGGCTGCGGCTGCG
- chr10-101010536-TGCTGCGGCTGCG-TGCTGCGGCTGCGGCTGCGGCTGCGGCTGCG
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP6_Very_Strong
The NM_001195263.2(PDZD7):c.2341_2352delCGCAGCCGCAGC(p.Arg781_Ser784del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000315 in 1,523,836 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000079 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000026 ( 0 hom. )
Consequence
PDZD7
NM_001195263.2 conservative_inframe_deletion
NM_001195263.2 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.894
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 Likely_benign. Variant got -6 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 10-101010536-TGCTGCGGCTGCG-T is Benign according to our data. Variant chr10-101010536-TGCTGCGGCTGCG-T is described in ClinVar as [Likely_benign]. Clinvar id is 1051760.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDZD7 | NM_001195263.2 | c.2341_2352delCGCAGCCGCAGC | p.Arg781_Ser784del | conservative_inframe_deletion | 15/17 | ENST00000619208.6 | NP_001182192.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDZD7 | ENST00000619208.6 | c.2341_2352delCGCAGCCGCAGC | p.Arg781_Ser784del | conservative_inframe_deletion | 15/17 | 5 | NM_001195263.2 | ENSP00000480489.1 | ||
PDZD7 | ENST00000474125.7 | n.*2288_*2299delCGCAGCCGCAGC | non_coding_transcript_exon_variant | 11/13 | 2 | ENSP00000474447.1 | ||||
PDZD7 | ENST00000474125.7 | n.*2288_*2299delCGCAGCCGCAGC | 3_prime_UTR_variant | 11/13 | 2 | ENSP00000474447.1 |
Frequencies
GnomAD3 genomes AF: 0.0000793 AC: 12AN: 151384Hom.: 0 Cov.: 0
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GnomAD3 exomes AF: 0.0000311 AC: 4AN: 128718Hom.: 0 AF XY: 0.0000430 AC XY: 3AN XY: 69728
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GnomAD4 exome AF: 0.0000262 AC: 36AN: 1372452Hom.: 0 AF XY: 0.0000252 AC XY: 17AN XY: 675328
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GnomAD4 genome AF: 0.0000793 AC: 12AN: 151384Hom.: 0 Cov.: 0 AF XY: 0.0000406 AC XY: 3AN XY: 73840
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 28, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 06, 2020 | This variant is associated with the following publications: (PMID: 31129248) - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at