rs13154602

Positions:

• chr5-77100092-C-A
• chr5-77100092-C-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.905+12473C>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 0.224 in 152,210 control chromosomes in the GnomAD database, including 4,537 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 0.22 (4537 hom., cov: 32)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: ZBED3-AS1 NR_182763.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500

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 (AMR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBED3-AS1	NR_182763.1	n.905+12473C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZBED3-AS1	ENST00000514114.5	n.157+12473C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34090 AN: 152084 Hom.: 4533 Cov.: 32

Gnomad AFR AF: 0.0781

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.232

GnomAD4 exome AF: 0.125 AC: 1 AN: 8 Hom.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

Gnomad4 NFE exome AF: 0.125

GnomAD4 genome AF: 0.224 AC: 34107 AN: 152202 Hom.: 4537 Cov.: 32 AF XY: 0.223 AC XY: 16567 AN XY: 74416

Gnomad4 AFR AF: 0.0782

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.230

Alfa AF: 0.214 Hom.: 726

Bravo AF: 0.228

Asia WGS AF: 0.195 AC: 676 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	1.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13154602; hg19: chr5-76395917;