rs7760666

Variant names:

• chr6-68911968-G-C
• rs7760666
• NM_001704.3:c.758-18591G>C

Variant summary

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

The NM_001704.3(ADGRB3):​c.758-18591G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,418 control chromosomes in the GnomAD database, including 8,291 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 0.32 (8291 hom., cov: 30)
• Consequence: ADGRB3 NM_001704.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 3 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRB3	NM_001704.3	c.758-18591G>C		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.758-18591G>C		intron_variant	Intron 3 of 31	1	NM_001704.3	ENSP00000359630.1
ADGRB3	ENST00000546190.5	c.758-18591G>C		intron_variant	Intron 1 of 29	1		ENSP00000441821.2
ADGRB3	ENST00000684661.1	n.758-18591G>C		intron_variant	Intron 3 of 31			ENSP00000507613.1

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48917 AN: 151300 Hom.: 8285 Cov.: 30

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.323 AC: 48959 AN: 151418 Hom.: 8291 Cov.: 30 AF XY: 0.319 AC XY: 23585 AN XY: 73982

African (AFR) AF: 0.291 AC: 12027 AN: 41266

American (AMR) AF: 0.281 AC: 4277 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1854 AN: 3464

East Asian (EAS) AF: 0.130 AC: 664 AN: 5122

South Asian (SAS) AF: 0.266 AC: 1275 AN: 4794

European-Finnish (FIN) AF: 0.284 AC: 2970 AN: 10442

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.363 AC: 24620 AN: 67822

Other (OTH) AF: 0.358 AC: 746 AN: 2084

Alfa AF: 0.330 Hom.: 1067

Bravo AF: 0.322

Asia WGS AF: 0.172 AC: 599 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.47
PhyloP100		-0.017
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: rs7760666; hg19: chr6-69621860;