X-153804167-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001303512.2(PDZD4):āc.1514A>Gā(p.Asn505Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00043 in 1,172,612 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 160 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001303512.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDZD4 | NM_001303512.2 | c.1514A>G | p.Asn505Ser | missense_variant | 8/8 | ENST00000393758.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZD4 | ENST00000393758.7 | c.1514A>G | p.Asn505Ser | missense_variant | 8/8 | 1 | NM_001303512.2 | P4 | |
PDZD4 | ENST00000164640.8 | c.1496A>G | p.Asn499Ser | missense_variant | 8/8 | 1 | A1 | ||
PDZD4 | ENST00000544474.5 | c.1169A>G | p.Asn390Ser | missense_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000142 AC: 16AN: 112291Hom.: 0 Cov.: 25 AF XY: 0.000116 AC XY: 4AN XY: 34559
GnomAD3 exomes AF: 0.000116 AC: 14AN: 120375Hom.: 0 AF XY: 0.0000917 AC XY: 3AN XY: 32729
GnomAD4 exome AF: 0.000460 AC: 488AN: 1060270Hom.: 0 Cov.: 33 AF XY: 0.000458 AC XY: 156AN XY: 340770
GnomAD4 genome ? AF: 0.000142 AC: 16AN: 112342Hom.: 0 Cov.: 25 AF XY: 0.000116 AC XY: 4AN XY: 34620
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | The c.1496A>G (p.N499S) alteration is located in exon 8 (coding exon 8) of the PDZD4 gene. This alteration results from a A to G substitution at nucleotide position 1496, causing the asparagine (N) at amino acid position 499 to be replaced by a serine (S). 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