chr10-117283947-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173791.5(PDZD8):c.2786A>G(p.Asn929Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,614,112 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173791.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDZD8 | NM_173791.5 | c.2786A>G | p.Asn929Ser | missense_variant | 5/5 | ENST00000334464.7 | |
PDZD8 | XM_005269518.5 | c.2663A>G | p.Asn888Ser | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZD8 | ENST00000334464.7 | c.2786A>G | p.Asn929Ser | missense_variant | 5/5 | 1 | NM_173791.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251346Hom.: 1 AF XY: 0.0000589 AC XY: 8AN XY: 135838
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461878Hom.: 1 Cov.: 34 AF XY: 0.0000234 AC XY: 17AN XY: 727240
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jan 29, 2024 | Variant summary: PDZD8 c.2786A>G (p.Asn929Ser) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00012 in 251346 control chromosomes in the gnomAD database, including 1 homozygotes. To our knowledge, no occurrence of c.2786A>G in individuals affected with Intellectual Developmental Disorder With Autism And Dysmorphic Facies and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as uncertain significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at