chr21-42732093-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002606.3(PDE9A):c.466G>A(p.Val156Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000179 in 1,614,212 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002606.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDE9A | NM_002606.3 | c.466G>A | p.Val156Met | missense_variant | 6/20 | ENST00000291539.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDE9A | ENST00000291539.11 | c.466G>A | p.Val156Met | missense_variant | 6/20 | 1 | NM_002606.3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000919 AC: 14AN: 152272Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000131 AC: 33AN: 251428Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135900
GnomAD4 exome AF: 0.000188 AC: 275AN: 1461822Hom.: 0 Cov.: 32 AF XY: 0.000182 AC XY: 132AN XY: 727206
GnomAD4 genome ? AF: 0.0000919 AC: 14AN: 152390Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74534
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2022 | The c.466G>A (p.V156M) alteration is located in exon 6 (coding exon 6) of the PDE9A gene. This alteration results from a G to A substitution at nucleotide position 466, causing the valine (V) at amino acid position 156 to be replaced by a methionine (M). 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