12-20369375-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000921.5(PDE3A):c.91C>T(p.His31Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000215 in 1,397,698 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 (★).
Frequency
Consequence
NM_000921.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDE3A | NM_000921.5 | c.91C>T | p.His31Tyr | missense_variant | Exon 1 of 16 | ENST00000359062.4 | NP_000912.3 | |
PDE3A | NM_001378407.1 | c.91C>T | p.His31Tyr | missense_variant | Exon 1 of 14 | NP_001365336.1 | ||
PDE3A | NM_001378408.1 | c.-938C>T | 5_prime_UTR_variant | Exon 1 of 18 | NP_001365337.1 | |||
PDE3A-AS1 | NR_186033.1 | n.416+466G>A | intron_variant | Intron 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000137 AC: 2AN: 145752Hom.: 0 AF XY: 0.0000128 AC XY: 1AN XY: 78238
GnomAD4 exome AF: 0.00000215 AC: 3AN: 1397698Hom.: 0 Cov.: 34 AF XY: 0.00000290 AC XY: 2AN XY: 689448
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.91C>T (p.H31Y) alteration is located in exon 1 (coding exon 1) of the PDE3A gene. This alteration results from a C to T substitution at nucleotide position 91, causing the histidine (H) at amino acid position 31 to be replaced by a tyrosine (Y). 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