5-77154365-T-C

Position:

• chr5-77154365-T-C

Variant summary

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

The NM_001414622.1(PDE8B):​c.-34+35844T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,230 control chromosomes in the GnomAD database, including 21,357 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 0.49 (21357 hom., cov: 33)
• Consequence: PDE8B NM_001414622.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243

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 = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE8B	NM_001414622.1	c.-34+35844T>C		intron_variant			NP_001401551.1
PDE8B	NM_001414623.1	c.-34+35844T>C		intron_variant			NP_001401552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZBED3-AS1	ENST00000508401.1	n.201-10996T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.487 AC: 74089 AN: 152112 Hom.: 21351 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.487 AC: 74093 AN: 152230 Hom.: 21357 Cov.: 33 AF XY: 0.497 AC XY: 36973 AN XY: 74436

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.877

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.518

Alfa AF: 0.576 Hom.: 12013

Bravo AF: 0.463

Asia WGS AF: 0.720 AC: 2501 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	9.5
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6864250; hg19: chr5-76450190;