chr6-68937194-G-A

Variant names:

• chr6-68937194-G-A
• rs2184723
• NM_001704.3:c.1030+514G>A

Variant summary

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

The NM_001704.3(ADGRB3):​c.1030+514G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,784 control chromosomes in the GnomAD database, including 9,553 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 0.34 (9553 hom., cov: 32)
• Consequence: ADGRB3 NM_001704.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 6 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001704.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRB3	NM_001704.3	MANE Select	c.1030+514G>A		intron	N/A	NP_001695.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRB3	ENST00000370598.6	TSL:1 MANE Select	c.1030+514G>A		intron	N/A	ENSP00000359630.1
	ADGRB3	ENST00000546190.5	TSL:1	c.1030+514G>A		intron	N/A	ENSP00000441821.2
	ADGRB3	ENST00000684661.1		n.1030+514G>A		intron	N/A	ENSP00000507613.1

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50939 AN: 151662 Hom.: 9550 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.336 AC: 50962 AN: 151784 Hom.: 9553 Cov.: 32 AF XY: 0.331 AC XY: 24531 AN XY: 74148

African (AFR) AF: 0.204 AC: 8427 AN: 41360

American (AMR) AF: 0.304 AC: 4638 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2024 AN: 3464

East Asian (EAS) AF: 0.130 AC: 668 AN: 5158

South Asian (SAS) AF: 0.292 AC: 1405 AN: 4814

European-Finnish (FIN) AF: 0.316 AC: 3318 AN: 10496

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29138 AN: 67922

Other (OTH) AF: 0.382 AC: 805 AN: 2110

Alfa AF: 0.395 Hom.: 4016

Bravo AF: 0.331

Asia WGS AF: 0.182 AC: 635 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.2
DANN	Benign	0.61
PhyloP100		-0.0020
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: rs2184723; hg19: chr6-69647086;