XM_047444688.1:c.74+1720A>G

Variant names:

• chr2-182714971-T-C
• rs288264
• XM_047444688.1:c.74+1720A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047444688.1(PDE1A):​c.74+1720A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 151,980 control chromosomes in the GnomAD database, including 32,660 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.65 (32660 hom., cov: 31)
• Consequence: PDE1A XM_047444688.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 4 publications found

Genes affected

PDE1A (HGNC:8774): (phosphodiesterase 1A) Cyclic nucleotide phosphodiesterases (PDEs) play a role in signal transduction by regulating intracellular cyclic nucleotide concentrations through hydrolysis of cAMP and/or cGMP to their respective nucleoside 5-prime monophosphates. Members of the PDE1 family, such as PDE1A, are Ca(2+)/calmodulin (see CALM1; MIM 114180)-dependent PDEs (CaM-PDEs) that are activated by calmodulin in the presence of Ca(2+) (Michibata et al., 2001 [PubMed 11342109]; Fidock et al., 2002 [PubMed 11747989]).[supplied by OMIM, Oct 2009]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99050 AN: 151862 Hom.: 32638 Cov.: 31

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.680

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.652 AC: 99109 AN: 151980 Hom.: 32660 Cov.: 31 AF XY: 0.649 AC XY: 48247 AN XY: 74290

African (AFR) AF: 0.710 AC: 29446 AN: 41448

American (AMR) AF: 0.570 AC: 8688 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2703 AN: 3470

East Asian (EAS) AF: 0.501 AC: 2576 AN: 5144

South Asian (SAS) AF: 0.678 AC: 3273 AN: 4824

European-Finnish (FIN) AF: 0.630 AC: 6648 AN: 10556

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43602 AN: 67970

Other (OTH) AF: 0.677 AC: 1429 AN: 2112

Alfa AF: 0.639 Hom.: 37924

Bravo AF: 0.644

Asia WGS AF: 0.603 AC: 2104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.74
PhyloP100		0.039

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs288264; hg19: chr2-183579698;