chr6-68725614-A-G

Variant names:

• chr6-68725614-A-G
• rs9342730
• NM_001704.3:c.757+86182A>G

Variant summary

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

The NM_001704.3(ADGRB3):​c.757+86182A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,536 control chromosomes in the GnomAD database, including 7,694 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 0.31 (7694 hom., cov: 32)
• Consequence: ADGRB3 NM_001704.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.728
• 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]

ENSG00000308231 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRB3	NM_001704.3	MANE Select	c.757+86182A>G		intron	N/A	NP_001695.2	O60242-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRB3	ENST00000370598.6	TSL:1 MANE Select	c.757+86182A>G		intron	N/A	ENSP00000359630.1	O60242-1
	ADGRB3	ENST00000546190.5	TSL:1	c.757+86182A>G		intron	N/A	ENSP00000441821.2	O60242-1
	ADGRB3	ENST00000684661.1		n.757+86182A>G		intron	N/A	ENSP00000507613.1	A0A804HJR2

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47581 AN: 151418 Hom.: 7688 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.314 AC: 47630 AN: 151536 Hom.: 7694 Cov.: 32 AF XY: 0.308 AC XY: 22786 AN XY: 74068

African (AFR) AF: 0.278 AC: 11504 AN: 41410

American (AMR) AF: 0.341 AC: 5171 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1119 AN: 3458

East Asian (EAS) AF: 0.218 AC: 1116 AN: 5114

South Asian (SAS) AF: 0.230 AC: 1111 AN: 4824

European-Finnish (FIN) AF: 0.298 AC: 3155 AN: 10588

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23455 AN: 67686

Other (OTH) AF: 0.326 AC: 685 AN: 2100

Alfa AF: 0.327 Hom.: 1555

Bravo AF: 0.321

Asia WGS AF: 0.205 AC: 714 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.64
PhyloP100		0.73
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: rs9342730; hg19: chr6-69435506;