5-77219999-A-G

Position:

• chr5-77219999-A-G

Variant summary

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

The NM_003719.5(PDE8B):​c.339+8735A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 152,026 control chromosomes in the GnomAD database, including 24,416 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 0.55 (24416 hom., cov: 32)
• Consequence: PDE8B NM_003719.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175

Genes affected

PDE8B (HGNC:8794): (phosphodiesterase 8B) The protein encoded by this gene is a cyclic nucleotide phosphodiesterase (PDE) that catalyzes the hydrolysis of the second messenger cAMP. The encoded protein, which does not hydrolyze cGMP, is resistant to several PDE inhibitors. Defects in this gene are a cause of autosomal dominant striatal degeneration (ADSD). Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jul 2010]

ENSG00000284762 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE8B	NM_003719.5	c.339+8735A>G		intron_variant		ENST00000264917.10	NP_003710.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDE8B	ENST00000264917.10	c.339+8735A>G		intron_variant		1	NM_003719.5	ENSP00000264917.6
ENSG00000284762	ENST00000646262.1	c.-33-91995A>G		intron_variant				ENSP00000493971.1

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83503 AN: 151908 Hom.: 24366 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.550 AC: 83615 AN: 152026 Hom.: 24416 Cov.: 32 AF XY: 0.553 AC XY: 41087 AN XY: 74306

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.839

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.556

Alfa AF: 0.456 Hom.: 21163

Bravo AF: 0.564

Asia WGS AF: 0.691 AC: 2404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	8.0
DANN	Benign	0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs9687206; hg19: chr5-76515824; COSMIC: COSV53746534;