NM_001704.3:c.1735-3263C>G

Variant names:

• chr6-68990505-C-G
• rs1415031
• NM_001704.3:c.1735-3263C>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.1735-3263C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 151,912 control chromosomes in the GnomAD database, including 6,191 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 0.28 (6191 hom., cov: 31)
• Consequence: ADGRB3 NM_001704.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329
• Publications: 4 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=-0.57).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 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.1735-3263C>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.1735-3263C>G		intron	N/A	ENSP00000359630.1	O60242-1
	ADGRB3	ENST00000546190.5	TSL:1	c.1735-3263C>G		intron	N/A	ENSP00000441821.2	O60242-1
	ADGRB3	ENST00000684661.1		n.1735-3263C>G		intron	N/A	ENSP00000507613.1	A0A804HJR2

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42490 AN: 151792 Hom.: 6189 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.280 AC: 42517 AN: 151912 Hom.: 6191 Cov.: 31 AF XY: 0.274 AC XY: 20333 AN XY: 74228

African (AFR) AF: 0.273 AC: 11322 AN: 41434

American (AMR) AF: 0.225 AC: 3430 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1619 AN: 3466

East Asian (EAS) AF: 0.103 AC: 529 AN: 5154

South Asian (SAS) AF: 0.204 AC: 986 AN: 4824

European-Finnish (FIN) AF: 0.253 AC: 2672 AN: 10548

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21094 AN: 67936

Other (OTH) AF: 0.286 AC: 605 AN: 2112

Alfa AF: 0.293 Hom.: 800

Bravo AF: 0.279

Asia WGS AF: 0.133 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	14
DANN	Benign	0.74
PhyloP100		0.33
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: rs1415031; hg19: chr6-69700397;