3-73383996-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_015009.3(PDZRN3):c.2570G>A(p.Ser857Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000138 in 1,590,016 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. S857R) has been classified as Uncertain significance.
Frequency
Consequence
NM_015009.3 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 |
---|---|---|---|---|---|---|---|
PDZRN3 | NM_015009.3 | c.2570G>A | p.Ser857Asn | missense_variant | 10/10 | ENST00000263666.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZRN3 | ENST00000263666.9 | c.2570G>A | p.Ser857Asn | missense_variant | 10/10 | 1 | NM_015009.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000217 AC: 5AN: 229978Hom.: 0 AF XY: 0.0000404 AC XY: 5AN XY: 123852
GnomAD4 exome AF: 0.0000139 AC: 20AN: 1437840Hom.: 0 Cov.: 31 AF XY: 0.0000196 AC XY: 14AN XY: 713306
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at