rs2359775

chr5-77175638-T-A

Variant summary

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

The NM_001414622.1(PDE8B):c.-34+57117T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,128 control chromosomes in the GnomAD database, including 9,875 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 0.31 (9875 hom., cov: 32)
• Consequence: PDE8B NM_001414622.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160

Genes affected

PDE8B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE8B	NM_001414622.1	c.-34+57117T>A		intron_variant
PDE8B	NM_001414623.1	c.-34+57117T>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47531 AN: 152010 Hom.: 9846 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.313 AC: 47609 AN: 152128 Hom.: 9875 Cov.: 32 AF XY: 0.320 AC XY: 23800 AN XY: 74376

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.305

Alfa AF: 0.240 Hom.: 731

Bravo AF: 0.327

Asia WGS AF: 0.518 AC: 1799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	13
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2359775; hg19: chr5-76471463;