chr12-20369318-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000921.5(PDE3A):c.34G>A(p.Asp12Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 1,544,406 control chromosomes in the GnomAD database, including 74,230 homozygotes. 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 Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000921.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDE3A | NM_000921.5 | c.34G>A | p.Asp12Asn | missense_variant | 1/16 | ENST00000359062.4 | |
PDE3A | NM_001378407.1 | c.34G>A | p.Asp12Asn | missense_variant | 1/14 | ||
PDE3A | NM_001378408.1 | c.-995G>A | 5_prime_UTR_variant | 1/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDE3A | ENST00000359062.4 | c.34G>A | p.Asp12Asn | missense_variant | 1/16 | 1 | NM_000921.5 | P1 | |
PDE3A-AS1 | ENST00000535755.1 | n.422+523C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.344 AC: 52207AN: 151872Hom.: 9567 Cov.: 32
GnomAD3 exomes AF: 0.287 AC: 40744AN: 142038Hom.: 6322 AF XY: 0.288 AC XY: 21920AN XY: 76074
GnomAD4 exome AF: 0.301 AC: 419779AN: 1392416Hom.: 64656 Cov.: 35 AF XY: 0.300 AC XY: 206105AN XY: 686078
GnomAD4 genome ? AF: 0.344 AC: 52233AN: 151990Hom.: 9574 Cov.: 32 AF XY: 0.343 AC XY: 25444AN XY: 74288
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at