chr2-182201650-C-CAAAAAAAA

Variant names:

• chr2-182201650-C-CAAAAAAAA
• rs56413404
• NM_001363871.4:c.1004+30_1004+37dupTTTTTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001363871.4(PDE1A):​c.1004+30_1004+37dupTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0016 (1 hom., cov: 0)
  • Exomes 𝑓: 0.0054 (23 hom.)
  • Failed GnomAD Quality Control
• Consequence: PDE1A NM_001363871.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.543

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDE1A	NM_001363871.4	c.1004+30_1004+37dupTTTTTTTT		intron_variant	Intron 9 of 14	ENST00000409365.6	NP_001350800.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDE1A	ENST00000409365.6	c.1004+37_1004+38insTTTTTTTT		intron_variant	Intron 9 of 14	5	NM_001363871.4	ENSP00000386767.1

Frequencies

GnomAD3 genomes AF: 0.00159 AC: 217 AN: 136732 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.000716

Gnomad AMI AF: 0.00113

Gnomad AMR AF: 0.00326

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000639

Gnomad SAS AF: 0.000702

Gnomad FIN AF: 0.00107

Gnomad MID AF: 0.00336

Gnomad NFE AF: 0.00200

Gnomad OTH AF: 0.00160

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00541 AC: 6094 AN: 1125974 Hom.: 23 Cov.: 25 AF XY: 0.00543 AC XY: 3047 AN XY: 561588

Gnomad4 AFR exome AF: 0.000844

Gnomad4 AMR exome AF: 0.0114

Gnomad4 ASJ exome AF: 0.00597

Gnomad4 EAS exome AF: 0.00994

Gnomad4 SAS exome AF: 0.00405

Gnomad4 FIN exome AF: 0.00979

Gnomad4 NFE exome AF: 0.00514

Gnomad4 OTH exome AF: 0.00563

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00159 AC: 217 AN: 136730 Hom.: 1 Cov.: 0 AF XY: 0.00129 AC XY: 84 AN XY: 65098

Gnomad4 AFR AF: 0.000715

Gnomad4 AMR AF: 0.00326

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000640

Gnomad4 SAS AF: 0.000706

Gnomad4 FIN AF: 0.00107

Gnomad4 NFE AF: 0.00200

Gnomad4 OTH AF: 0.00159

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56413404; hg19: chr2-183066377;