rs555444131
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PM4_SupportingBP6BS1BS2
The NM_001195263.2(PDZD7):c.1348_1350delGAG(p.Glu450del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000747 in 1,613,768 control chromosomes in the GnomAD database, including 8 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001195263.2 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000421 AC: 64AN: 152016Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000907 AC: 228AN: 251294Hom.: 3 AF XY: 0.00121 AC XY: 164AN XY: 135842
GnomAD4 exome AF: 0.000781 AC: 1141AN: 1461634Hom.: 8 AF XY: 0.000941 AC XY: 684AN XY: 727114
GnomAD4 genome AF: 0.000421 AC: 64AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74378
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:3
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PDZD7: PM4:Supporting, BS1 -
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Retinal dystrophy Uncertain:1
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not specified Benign:1
Glu450del in exon 9 of PDZD7: This variant is not expected to have clinical sign ificance due to a lack of conservation across species, including mammals. Of no te, the marmoset has an in-frame deletion of the glutamate (Glu) at this positio n. -
PDZD7-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at