chr3-73383995-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS2_Supporting
The NM_015009.3(PDZRN3):c.2571C>A(p.Ser857Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000348 in 1,437,202 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict 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. S857N) 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 -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDZRN3 | NM_015009.3 | c.2571C>A | p.Ser857Arg | missense_variant | 10/10 | ENST00000263666.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZRN3 | ENST00000263666.9 | c.2571C>A | p.Ser857Arg | missense_variant | 10/10 | 1 | NM_015009.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000174 AC: 4AN: 229312Hom.: 0 AF XY: 0.0000162 AC XY: 2AN XY: 123494
GnomAD4 exome AF: 0.00000348 AC: 5AN: 1437202Hom.: 0 Cov.: 31 AF XY: 0.00000421 AC XY: 3AN XY: 712964
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.2571C>A (p.S857R) alteration is located in exon 10 (coding exon 10) of the PDZRN3 gene. This alteration results from a C to A substitution at nucleotide position 2571, causing the serine (S) at amino acid position 857 to be replaced by an arginine (R). 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