rs4704389

Positions:

• chr5-77150278-A-G

Variant summary

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

The ENST00000514114.5(ZBED3-AS1):​n.360-946A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 152,018 control chromosomes in the GnomAD database, including 22,624 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 0.52 (22624 hom., cov: 32)
• Consequence: ZBED3-AS1 ENST00000514114.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

Genes affected

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

PDE8B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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	UniProt
PDE8B	NM_001414622.1	c.-34+31757A>G		intron_variant
PDE8B	NM_001414623.1	c.-34+31757A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBED3-AS1	ENST00000514114.5	n.360-946A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79539 AN: 151898 Hom.: 22613 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.523 AC: 79561 AN: 152018 Hom.: 22624 Cov.: 32 AF XY: 0.532 AC XY: 39532 AN XY: 74302

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.877

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.548

Alfa AF: 0.527 Hom.: 3264

Bravo AF: 0.506

Asia WGS AF: 0.727 AC: 2527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4704389; hg19: chr5-76446103;