rs4457053

Positions:

• chr5-77129124-G-A
• chr5-77129124-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+10603G>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 0.743 in 151,998 control chromosomes in the GnomAD database, including 42,433 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 0.74 (42433 hom., cov: 30)
• Consequence: ZBED3-AS1 NR_182763.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

Genes affected

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

LOC124901008 (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	Protein	UniProt
ZBED3-AS1	NR_182763.1	n.1107+10603G>A		intron_variant, non_coding_transcript_variant
LOC124901008	XR_007058827.1	n.136+696C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZBED3-AS1	ENST00000514114.5	n.359+10603G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112882 AN: 151880 Hom.: 42392 Cov.: 30

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.743 AC: 112980 AN: 151998 Hom.: 42433 Cov.: 30 AF XY: 0.749 AC XY: 55609 AN XY: 74264

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.948

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.717

Alfa AF: 0.697 Hom.: 48114

Bravo AF: 0.735

Asia WGS AF: 0.858 AC: 2980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.86
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4457053; hg19: chr5-76424949;