5-31799663-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BS2
The NM_178140.4(PDZD2):c.415C>T(p.Arg139Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000613 in 1,613,854 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R139Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_178140.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDZD2 | NM_178140.4 | c.415C>T | p.Arg139Trp | missense_variant | 2/25 | ENST00000438447.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZD2 | ENST00000438447.2 | c.415C>T | p.Arg139Trp | missense_variant | 2/25 | 1 | NM_178140.4 | P1 | |
PDZD2 | ENST00000502824.1 | n.863C>T | non_coding_transcript_exon_variant | 2/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248650Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134632
GnomAD4 exome AF: 0.0000643 AC: 94AN: 1461774Hom.: 1 Cov.: 32 AF XY: 0.0000674 AC XY: 49AN XY: 727182
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74272
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2022 | The c.415C>T (p.R139W) alteration is located in exon 1 (coding exon 1) of the PDZD2 gene. This alteration results from a C to T substitution at nucleotide position 415, causing the arginine (R) at amino acid position 139 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at