3-73384234-A-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_015009.3(PDZRN3):c.2332T>A(p.Ser778Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000049 in 1,613,434 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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. S778Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_015009.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDZRN3 | NM_015009.3 | c.2332T>A | p.Ser778Thr | missense_variant | 10/10 | ENST00000263666.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZRN3 | ENST00000263666.9 | c.2332T>A | p.Ser778Thr | missense_variant | 10/10 | 1 | NM_015009.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152022Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250300Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135512
GnomAD4 exome AF: 0.0000534 AC: 78AN: 1461412Hom.: 0 Cov.: 38 AF XY: 0.0000468 AC XY: 34AN XY: 727040
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152022Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74248
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2021 | The c.2332T>A (p.S778T) alteration is located in exon 10 (coding exon 10) of the PDZRN3 gene. This alteration results from a T to A substitution at nucleotide position 2332, causing the serine (S) at amino acid position 778 to be replaced by a threonine (T). 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