chr5-77166328-C-G

Position:

• chr5-77166328-C-G

Variant summary

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

The NM_001414622.1(PDE8B):​c.-34+47807C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 151,898 control chromosomes in the GnomAD database, including 44,706 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 0.76 (44706 hom., cov: 29)
• Consequence: PDE8B NM_001414622.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801

Genes affected

PDE8B (HGNC:):

ZBED3-AS1 (HGNC:44188): (ZBED3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE8B	NM_001414622.1	c.-34+47807C>G		intron_variant
PDE8B	NM_001414623.1	c.-34+47807C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBED3-AS1	ENST00000508401.1	n.341-340C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115595 AN: 151780 Hom.: 44661 Cov.: 29

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.762 AC: 115694 AN: 151898 Hom.: 44706 Cov.: 29 AF XY: 0.769 AC XY: 57097 AN XY: 74242

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.747

Alfa AF: 0.744 Hom.: 5266

Bravo AF: 0.750

Asia WGS AF: 0.886 AC: 3082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4361497; hg19: chr5-76462153;