rs6878122

Positions:

• chr5-77131486-G-A
• chr5-77131486-G-C
• chr5-77131486-G-T

Variant summary

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

The NR_182763.1(ZBED3-AS1):​n.1107+12965G>A 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 0.756 in 152,124 control chromosomes in the GnomAD database, including 44,156 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 (44156 hom., cov: 31)
• Consequence: ZBED3-AS1 NR_182763.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBED3-AS1	NR_182763.1	n.1107+12965G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBED3-AS1	ENST00000514114.5	n.359+12965G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114958 AN: 152006 Hom.: 44111 Cov.: 31

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.756 AC: 115059 AN: 152124 Hom.: 44156 Cov.: 31 AF XY: 0.762 AC XY: 56637 AN XY: 74368

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.949

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.728

Alfa AF: 0.729 Hom.: 5042

Bravo AF: 0.750

Asia WGS AF: 0.873 AC: 3032 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6878122; hg19: chr5-76427311;