rs2928163

Positions:

• chr5-77192420-G-A
• chr5-77192420-G-T

Variant summary

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

The NM_001349750.3(PDE8B):​c.36+11934G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.722 in 152,092 control chromosomes in the GnomAD database, including 40,617 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 0.72 (40617 hom., cov: 31)
• Consequence: PDE8B NM_001349750.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

Genes affected

PDE8B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE8B	NM_001349750.3	c.36+11934G>A		intron_variant			NP_001336679.1
PDE8B	NM_001349752.3	c.36+11934G>A		intron_variant			NP_001336681.1
PDE8B	NM_001376062.1	c.36+11934G>A		intron_variant			NP_001362991.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109688 AN: 151974 Hom.: 40562 Cov.: 31

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.722 AC: 109803 AN: 152092 Hom.: 40617 Cov.: 31 AF XY: 0.728 AC XY: 54152 AN XY: 74342

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.707

Alfa AF: 0.701 Hom.: 7069

Bravo AF: 0.713

Asia WGS AF: 0.870 AC: 3026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.40
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2928163; hg19: chr5-76488245;