rs1880177

Variant names:

• chr6-68880064-G-A
• rs1880177
• NM_001704.3:c.758-50495G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-68880064-G-A
• chr6-68880064-G-T

Variant summary

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

The NM_001704.3(ADGRB3):​c.758-50495G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 152,098 control chromosomes in the GnomAD database, including 884 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 0.094 (884 hom., cov: 32)
• Consequence: ADGRB3 NM_001704.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 2 publications found

Genes affected

ADGRB3 (HGNC:945): (adhesion G protein-coupled receptor B3) This p53-target gene encodes a brain-specific angiogenesis inhibitor, a seven-span transmembrane protein, and is thought to be a member of the secretin receptor family. Brain-specific angiogenesis proteins BAI2 and BAI3 are similar to BAI1 in structure, have similar tissue specificities, and may also play a role in angiogenesis. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRB3	NM_001704.3	c.758-50495G>A		intron_variant	Intron 3 of 31	ENST00000370598.6	NP_001695.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRB3	ENST00000370598.6	c.758-50495G>A		intron_variant	Intron 3 of 31	1	NM_001704.3	ENSP00000359630.1
ADGRB3	ENST00000546190.5	c.758-50495G>A		intron_variant	Intron 1 of 29	1		ENSP00000441821.2
ADGRB3	ENST00000684661.1	n.758-50495G>A		intron_variant	Intron 3 of 31			ENSP00000507613.1

Frequencies

GnomAD3 genomes AF: 0.0938 AC: 14260 AN: 151980 Hom.: 884 Cov.: 32

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0751

Gnomad ASJ AF: 0.0478

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.0858

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

GnomAD4 genome AF: 0.0937 AC: 14250 AN: 152098 Hom.: 884 Cov.: 32 AF XY: 0.0964 AC XY: 7168 AN XY: 74342

African (AFR) AF: 0.0235 AC: 976 AN: 41510

American (AMR) AF: 0.0748 AC: 1143 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0478 AC: 166 AN: 3472

East Asian (EAS) AF: 0.0108 AC: 56 AN: 5170

South Asian (SAS) AF: 0.108 AC: 519 AN: 4814

European-Finnish (FIN) AF: 0.201 AC: 2127 AN: 10562

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9025 AN: 67970

Other (OTH) AF: 0.0844 AC: 178 AN: 2108

Alfa AF: 0.110 Hom.: 199

Bravo AF: 0.0789

Asia WGS AF: 0.0470 AC: 162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.68
DANN	Benign	0.63
PhyloP100		-0.25
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: rs1880177; hg19: chr6-69589956;