13-77807011-G-T

Variant names:

• chr13-77807011-G-T
• rs975739
• ENST00000667150.1:n.67-2906G>T

Variant summary

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

The ENST00000667150.1(EDNRB-AS1):​n.67-2906G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 152,096 control chromosomes in the GnomAD database, including 23,193 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 0.55 (23193 hom., cov: 33)
• Consequence: EDNRB-AS1 ENST00000667150.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.760
• Publications: 13 publications found

Genes affected

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

ENSG00000294543 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667150.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EDNRB-AS1	ENST00000667150.1		n.67-2906G>T		intron	N/A
	EDNRB-AS1	ENST00000724134.1		n.67-2906G>T		intron	N/A
	ENSG00000294543	ENST00000724302.1		n.811+24584C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83079 AN: 151978 Hom.: 23196 Cov.: 33

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.546 AC: 83107 AN: 152096 Hom.: 23193 Cov.: 33 AF XY: 0.539 AC XY: 40056 AN XY: 74364

African (AFR) AF: 0.510 AC: 21159 AN: 41484

American (AMR) AF: 0.513 AC: 7826 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1715 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1229 AN: 5178

South Asian (SAS) AF: 0.406 AC: 1958 AN: 4824

European-Finnish (FIN) AF: 0.569 AC: 6019 AN: 10570

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41301 AN: 67994

Other (OTH) AF: 0.545 AC: 1152 AN: 2114

Alfa AF: 0.574 Hom.: 42542

Bravo AF: 0.540

Asia WGS AF: 0.351 AC: 1221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.56
DANN	Benign	0.57
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs975739; hg19: chr13-78381146;