chr6-69002009-A-G

Variant names:

• chr6-69002009-A-G
• rs9446083
• NM_001704.3:c.1929+8047A>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.1929+8047A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,970 control chromosomes in the GnomAD database, including 13,642 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 0.40 (13642 hom., cov: 32)
• Consequence: ADGRB3 NM_001704.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.655
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 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.1929+8047A>G		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.1929+8047A>G		intron	N/A	ENSP00000359630.1
	ADGRB3	ENST00000546190.5	TSL:1	c.1929+8047A>G		intron	N/A	ENSP00000441821.2
	ADGRB3	ENST00000684661.1		n.1929+8047A>G		intron	N/A	ENSP00000507613.1

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60538 AN: 151852 Hom.: 13643 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.0592

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.398 AC: 60537 AN: 151970 Hom.: 13642 Cov.: 32 AF XY: 0.395 AC XY: 29321 AN XY: 74276

African (AFR) AF: 0.244 AC: 10125 AN: 41446

American (AMR) AF: 0.329 AC: 5032 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2320 AN: 3466

East Asian (EAS) AF: 0.0593 AC: 306 AN: 5160

South Asian (SAS) AF: 0.351 AC: 1689 AN: 4810

European-Finnish (FIN) AF: 0.499 AC: 5263 AN: 10542

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34431 AN: 67958

Other (OTH) AF: 0.413 AC: 873 AN: 2112

Alfa AF: 0.474 Hom.: 24118

Bravo AF: 0.379

Asia WGS AF: 0.169 AC: 587 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.3
DANN	Benign	0.78
PhyloP100		0.66
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: rs9446083; hg19: chr6-69711901;