rs3823064

Variant names:

• chr6-68971725-A-G
• rs3823064
• NM_001704.3:c.1526-3038A>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.1526-3038A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 152,164 control chromosomes in the GnomAD database, including 19,391 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 0.49 (19391 hom., cov: 33)
• Consequence: ADGRB3 NM_001704.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRB3	NM_001704.3	c.1526-3038A>G		intron_variant	Intron 8 of 31	ENST00000370598.6	NP_001695.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRB3	ENST00000370598.6	c.1526-3038A>G		intron_variant	Intron 8 of 31	1	NM_001704.3	ENSP00000359630.1
ADGRB3	ENST00000546190.5	c.1526-3038A>G		intron_variant	Intron 6 of 29	1		ENSP00000441821.2
ADGRB3	ENST00000684661.1	n.1526-3038A>G		intron_variant	Intron 8 of 31			ENSP00000507613.1

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74518 AN: 152046 Hom.: 19355 Cov.: 33

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.490 AC: 74603 AN: 152164 Hom.: 19391 Cov.: 33 AF XY: 0.488 AC XY: 36274 AN XY: 74392

African (AFR) AF: 0.652 AC: 27054 AN: 41508

American (AMR) AF: 0.442 AC: 6759 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1932 AN: 3472

East Asian (EAS) AF: 0.682 AC: 3524 AN: 5168

South Asian (SAS) AF: 0.423 AC: 2041 AN: 4828

European-Finnish (FIN) AF: 0.385 AC: 4080 AN: 10584

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27618 AN: 67984

Other (OTH) AF: 0.495 AC: 1046 AN: 2114

Alfa AF: 0.452 Hom.: 41757

Bravo AF: 0.505

Asia WGS AF: 0.563 AC: 1958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.37
PhyloP100		-0.51
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: rs3823064; hg19: chr6-69681617;