rs7708285

chr5-77130042-G-Achr5-77130042-G-C

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+11521G>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 0.763 in 152,158 control chromosomes in the GnomAD database, including 44,923 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 (44923 hom., cov: 32)
• Consequence: ZBED3-AS1 NR_182763.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.928

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=-0.87).
• 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+11521G>A		intron_variant, non_coding_transcript_variant
LOC124901008	XR_007058827.1	n.73-159C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBED3-AS1	ENST00000514114.5	n.359+11521G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.763 AC: 116050 AN: 152040 Hom.: 44878 Cov.: 32

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.763 AC: 116152 AN: 152158 Hom.: 44923 Cov.: 32 AF XY: 0.768 AC XY: 57175 AN XY: 74404

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.948

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.735

Alfa AF: 0.714 Hom.: 45128

Bravo AF: 0.756

Asia WGS AF: 0.877 AC: 3047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.0
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7708285; hg19: chr5-76425867;