rs10507875

Positions:

• chr13-77943119-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435281.2(ENSG00000233379):​n.138+1686T>C 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 0.173 in 152,104 control chromosomes in the GnomAD database, including 2,735 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 0.17 (2735 hom., cov: 33)
• Consequence: ENST00000435281.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295

Genes affected

(HGNC:):

OBI1-AS1 (HGNC:42700): (OBI1 antisense RNA 1)

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EDNRB	NM_000115.5	c.-51-24495T>C		intron_variant			NP_000106.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000435281.2	n.138+1686T>C		intron_variant, non_coding_transcript_variant		5
OBI1-AS1	ENST00000607862.5	n.230+23201A>G		intron_variant, non_coding_transcript_variant		1
EDNRB	ENST00000646948.1	c.-51-24495T>C		intron_variant				ENSP00000493895	P1
	ENST00000662890.1	n.134+1686T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26302 AN: 151986 Hom.: 2734 Cov.: 33

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.173 AC: 26313 AN: 152104 Hom.: 2735 Cov.: 33 AF XY: 0.179 AC XY: 13287 AN XY: 74340

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.168

Alfa AF: 0.152 Hom.: 1706

Bravo AF: 0.179

Asia WGS AF: 0.310 AC: 1075 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507875; hg19: chr13-78517254;