rs3818416

Variant names:

• chr13-77900333-A-C
• rs3818416
• NM_001122659.3:c.1085+188T>G

Your query was ambiguous. Multiple possible variants found:

• chr13-77900333-A-C
• chr13-77900333-A-G
• chr13-77900333-A-T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001122659.3(EDNRB):​c.1085+188T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 151,704 control chromosomes in the GnomAD database, including 42,780 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.75 (42780 hom., cov: 31)
• Consequence: EDNRB NM_001122659.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.350
• Publications: 25 publications found

Genes affected

EDNRB (HGNC:3180): (endothelin receptor type B) The protein encoded by this gene is a G protein-coupled receptor which activates a phosphatidylinositol-calcium second messenger system. Its ligand, endothelin, consists of a family of three potent vasoactive peptides: ET1, ET2, and ET3. Studies suggest that the multigenic disorder, Hirschsprung disease type 2, is due to mutations in the endothelin receptor type B gene. Alternative splicing and the use of alternative promoters results in multiple transcript variants. [provided by RefSeq, Oct 2016]

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

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 13-77900333-A-C is Benign according to our data. Variant chr13-77900333-A-C is described in ClinVar as Benign. ClinVar VariationId is 1246466.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001122659.3. 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
	EDNRB	NM_001122659.3	MANE Select	c.1085+188T>G		intron	N/A	NP_001116131.1	P24530-1
	EDNRB	NM_001201397.2		c.1355+188T>G		intron	N/A	NP_001188326.1	P24530-3
	EDNRB	NM_000115.5		c.1085+188T>G		intron	N/A	NP_000106.1	P24530-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EDNRB	ENST00000646607.2	MANE Select	c.1085+188T>G		intron	N/A	ENSP00000493527.1	P24530-1
	EDNRB	ENST00000377211.8	TSL:1	c.1355+188T>G		intron	N/A	ENSP00000366416.4	P24530-3
	EDNRB	ENST00000626030.1	TSL:1	c.1085+188T>G		intron	N/A	ENSP00000486202.1	P24530-2

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113514 AN: 151586 Hom.: 42767 Cov.: 31

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.749 AC: 113569 AN: 151704 Hom.: 42780 Cov.: 31 AF XY: 0.751 AC XY: 55626 AN XY: 74116

African (AFR) AF: 0.679 AC: 28118 AN: 41406

American (AMR) AF: 0.807 AC: 12271 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2193 AN: 3460

East Asian (EAS) AF: 0.885 AC: 4519 AN: 5108

South Asian (SAS) AF: 0.783 AC: 3760 AN: 4804

European-Finnish (FIN) AF: 0.774 AC: 8173 AN: 10562

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52142 AN: 67856

Other (OTH) AF: 0.731 AC: 1537 AN: 2102

Alfa AF: 0.758 Hom.: 64386

Bravo AF: 0.749

Asia WGS AF: 0.794 AC: 2760 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.74
DANN	Benign	0.30
PhyloP100		-0.35
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3818416; hg19: chr13-78474468;