rs1880916

Positions:

• chr2-177930703-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016953.4(PDE11A):​c.1072-25516C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,138 control chromosomes in the GnomAD database, including 3,783 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 0.22 (3783 hom., cov: 33)
• Consequence: PDE11A NM_016953.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

Genes affected

PDE11A (HGNC:8773): (phosphodiesterase 11A) The 3',5'-cyclic nucleotides cAMP and cGMP function as second messengers in a wide variety of signal transduction pathways. 3',5'-cyclic nucleotide phosphodiesterases (PDEs) catalyze the hydrolysis of cAMP and cGMP to the corresponding 5'-monophosphates and provide a mechanism to downregulate cAMP and cGMP signaling. This gene encodes a member of the PDE protein superfamily. Mutations in this gene are a cause of Cushing disease and adrenocortical hyperplasia. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE11A	NM_016953.4	c.1072-25516C>T		intron_variant		ENST00000286063.11	NP_058649.3
PDE11A	NM_001077197.2	c.322-25516C>T		intron_variant			NP_001070665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDE11A	ENST00000286063.11	c.1072-25516C>T		intron_variant		1	NM_016953.4	ENSP00000286063	P1
PDE11A	ENST00000358450.8	c.322-25516C>T		intron_variant		1		ENSP00000351232

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33425 AN: 152020 Hom.: 3785 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.220 AC: 33438 AN: 152138 Hom.: 3783 Cov.: 33 AF XY: 0.220 AC XY: 16364 AN XY: 74360

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.245

Alfa AF: 0.211 Hom.: 1973

Bravo AF: 0.223

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1880916; hg19: chr2-178795430;