chr13-77800045-A-T

Variant names:

• chr13-77800045-A-T
• rs1279386
• ENST00000667150.1:n.67-9872A>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.67-9872A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,922 control chromosomes in the GnomAD database, including 21,416 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 0.53 (21416 hom., cov: 32)
• Consequence: EDNRB-AS1 ENST00000667150.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EDNRB-AS1	ENST00000667150.1	n.67-9872A>T		intron_variant	Intron 1 of 4
EDNRB-AS1	ENST00000724134.1	n.67-9872A>T		intron_variant	Intron 1 of 3
ENSG00000294543	ENST00000724302.1	n.811+31550T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.527 AC: 79926 AN: 151804 Hom.: 21419 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.526 AC: 79957 AN: 151922 Hom.: 21416 Cov.: 32 AF XY: 0.519 AC XY: 38556 AN XY: 74238

African (AFR) AF: 0.500 AC: 20721 AN: 41408

American (AMR) AF: 0.507 AC: 7728 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1536 AN: 3470

East Asian (EAS) AF: 0.247 AC: 1279 AN: 5176

South Asian (SAS) AF: 0.401 AC: 1930 AN: 4808

European-Finnish (FIN) AF: 0.551 AC: 5808 AN: 10534

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39121 AN: 67964

Other (OTH) AF: 0.520 AC: 1099 AN: 2112

Alfa AF: 0.555 Hom.: 2929

Bravo AF: 0.521

Asia WGS AF: 0.352 AC: 1224 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.066
DANN	Benign	0.76
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1279386; hg19: chr13-78374180;