chr6-69320088-C-A

Variant names:

• chr6-69320088-C-A
• rs1290329
• NM_001704.3:c.2815-4784C>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.2815-4784C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 150,882 control chromosomes in the GnomAD database, including 17,209 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 0.45 (17209 hom., cov: 31)
• Consequence: ADGRB3 NM_001704.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRB3	NM_001704.3	c.2815-4784C>A		intron_variant	Intron 20 of 31	ENST00000370598.6	NP_001695.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRB3	ENST00000370598.6	c.2815-4784C>A		intron_variant	Intron 20 of 31	1	NM_001704.3	ENSP00000359630.1

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67520 AN: 150764 Hom.: 17177 Cov.: 31

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.448 AC: 67603 AN: 150882 Hom.: 17209 Cov.: 31 AF XY: 0.438 AC XY: 32306 AN XY: 73706

African (AFR) AF: 0.691 AC: 28538 AN: 41328

American (AMR) AF: 0.441 AC: 6659 AN: 15110

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1425 AN: 3450

East Asian (EAS) AF: 0.163 AC: 837 AN: 5140

South Asian (SAS) AF: 0.226 AC: 1087 AN: 4806

European-Finnish (FIN) AF: 0.305 AC: 3171 AN: 10404

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.366 AC: 24680 AN: 67354

Other (OTH) AF: 0.435 AC: 909 AN: 2088

Alfa AF: 0.388 Hom.: 6460

Bravo AF: 0.471

Asia WGS AF: 0.208 AC: 717 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.087
DANN	Benign	0.48
PhyloP100		-0.79
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: rs1290329; hg19: chr6-70029980;