5-77181995-A-G

Position:

• chr5-77181995-A-G

Variant summary

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

The NM_001349750.3(PDE8B):​c.36+1509A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 151,806 control chromosomes in the GnomAD database, including 7,136 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 0.26 (7136 hom., cov: 31)
• Consequence: PDE8B NM_001349750.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.03

Genes affected

PDE8B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE8B	NM_001349750.3	c.36+1509A>G		intron_variant
PDE8B	NM_001349752.3	c.36+1509A>G		intron_variant
PDE8B	NM_001376062.1	c.36+1509A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39459 AN: 151688 Hom.: 7118 Cov.: 31

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.260 AC: 39534 AN: 151806 Hom.: 7136 Cov.: 31 AF XY: 0.270 AC XY: 19997 AN XY: 74200

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.822

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.245

Alfa AF: 0.176 Hom.: 604

Bravo AF: 0.273

Asia WGS AF: 0.533 AC: 1852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	17
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2928167; hg19: chr5-76477820;