chr12-20369514-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000921.5(PDE3A):c.230T>A(p.Leu77Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000213 in 1,408,036 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. L77L) has been classified as Benign.
Frequency
Consequence
NM_000921.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDE3A | NM_000921.5 | c.230T>A | p.Leu77Gln | missense_variant | 1/16 | ENST00000359062.4 | |
PDE3A | NM_001378407.1 | c.230T>A | p.Leu77Gln | missense_variant | 1/14 | ||
PDE3A | NM_001378408.1 | c.-799T>A | 5_prime_UTR_variant | 1/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDE3A | ENST00000359062.4 | c.230T>A | p.Leu77Gln | missense_variant | 1/16 | 1 | NM_000921.5 | P1 | |
PDE3A-AS1 | ENST00000535755.1 | n.422+327A>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000183 AC: 3AN: 163732Hom.: 0 AF XY: 0.0000228 AC XY: 2AN XY: 87616
GnomAD4 exome AF: 0.00000213 AC: 3AN: 1408036Hom.: 0 Cov.: 34 AF XY: 0.00000288 AC XY: 2AN XY: 695140
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2024 | The c.230T>A (p.L77Q) alteration is located in exon 1 (coding exon 1) of the PDE3A gene. This alteration results from a T to A substitution at nucleotide position 230, causing the leucine (L) at amino acid position 77 to be replaced by a glutamine (Q). 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