13-77888588-A-G

Variant names:

• chr13-77888588-A-G
• rs1924921
• ENST00000724134.1:n.327-19104A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000724134.1(EDNRB-AS1):​n.327-19104A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 151,824 control chromosomes in the GnomAD database, including 60,976 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 0.90 (60976 hom., cov: 29)
• Consequence: EDNRB-AS1 ENST00000724134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 3 publications found

Genes affected

EDNRB-AS1 (HGNC:49045): (EDNRB antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000724134.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EDNRB-AS1	NR_103853.1		n.1695-19104A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EDNRB-AS1	ENST00000724134.1		n.327-19104A>G		intron	N/A
	EDNRB-AS1	ENST00000724135.1		n.462-11597A>G		intron	N/A
	EDNRB-AS1	ENST00000724136.1		n.100-19104A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.896 AC: 135896 AN: 151706 Hom.: 60930 Cov.: 29

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.896 AC: 135999 AN: 151824 Hom.: 60976 Cov.: 29 AF XY: 0.897 AC XY: 66550 AN XY: 74190

African (AFR) AF: 0.910 AC: 37690 AN: 41404

American (AMR) AF: 0.904 AC: 13727 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2922 AN: 3468

East Asian (EAS) AF: 0.977 AC: 5030 AN: 5150

South Asian (SAS) AF: 0.931 AC: 4480 AN: 4810

European-Finnish (FIN) AF: 0.883 AC: 9334 AN: 10566

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.882 AC: 59923 AN: 67932

Other (OTH) AF: 0.888 AC: 1870 AN: 2106

Alfa AF: 0.883 Hom.: 3133

Bravo AF: 0.898

Asia WGS AF: 0.927 AC: 3224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.68
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1924921; hg19: chr13-78462723;