6-68725614-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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]

LOC124901492 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRB3	NM_001704.3	c.757+86182A>G		intron_variant	Intron 3 of 31	ENST00000370598.6	NP_001695.2
LOC124901492	XR_007059925.1	n.203+1431T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRB3	ENST00000370598.6	c.757+86182A>G		intron_variant	Intron 3 of 31	1	NM_001704.3	ENSP00000359630.1
ADGRB3	ENST00000546190.5	c.757+86182A>G		intron_variant	Intron 1 of 29	1		ENSP00000441821.2
ADGRB3	ENST00000684661.1	n.757+86182A>G		intron_variant	Intron 3 of 31			ENSP00000507613.1

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

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.326

Alfa AF: 0.328 Hom.: 1521

Bravo AF: 0.321

Asia WGS AF: 0.205 AC: 714 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.64

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

Publications

LitVar

Other links and lift over

dbSNP: rs9342730; hg19: chr6-69435506;