10-101010536-T-TGCTGCG
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_001195263.2(PDZD7):c.2347_2352dupCGCAGC(p.Ser784_Ser785insArgSer) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 1,523,516 control chromosomes in the GnomAD database, including 154,616 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001195263.2 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDZD7 | ENST00000619208.6 | c.2347_2352dupCGCAGC | p.Ser784_Ser785insArgSer | conservative_inframe_insertion | Exon 15 of 17 | 5 | NM_001195263.2 | ENSP00000480489.1 | ||
PDZD7 | ENST00000474125.7 | n.*2294_*2299dupCGCAGC | non_coding_transcript_exon_variant | Exon 11 of 13 | 2 | ENSP00000474447.1 | ||||
PDZD7 | ENST00000474125.7 | n.*2294_*2299dupCGCAGC | 3_prime_UTR_variant | Exon 11 of 13 | 2 | ENSP00000474447.1 |
Frequencies
GnomAD3 genomes AF: 0.360 AC: 54483AN: 151212Hom.: 11808 Cov.: 0
GnomAD3 exomes AF: 0.383 AC: 49335AN: 128718Hom.: 10799 AF XY: 0.388 AC XY: 27044AN XY: 69728
GnomAD4 exome AF: 0.446 AC: 612106AN: 1372190Hom.: 142810 Cov.: 98 AF XY: 0.445 AC XY: 300439AN XY: 675136
GnomAD4 genome AF: 0.360 AC: 54487AN: 151326Hom.: 11806 Cov.: 0 AF XY: 0.359 AC XY: 26538AN XY: 73868
ClinVar
Submissions by phenotype
not specified Benign:4
- -
Arg783_Ser784dup in exon 15A of PDZD7: This variant is not expected to have clin ical significance because it has been identified in 27% (584/2178) of chromosome s from a broad population (1000Genomes, dbSNP rs200896335). -
- -
- -
not provided Benign:2
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. -
- -
Usher syndrome type 2C Benign:1
- -
Hearing loss, autosomal recessive 57 Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at