NM_001704.3:c.2108-11049A>G

Variant names:

• chr6-69037136-A-G
• rs7743332
• NM_001704.3:c.2108-11049A>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.2108-11049A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,886 control chromosomes in the GnomAD database, including 14,381 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 0.42 (14381 hom., cov: 31)
• Consequence: ADGRB3 NM_001704.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRB3	NM_001704.3	c.2108-11049A>G		intron_variant	Intron 13 of 31	ENST00000370598.6	NP_001695.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRB3	ENST00000370598.6	c.2108-11049A>G		intron_variant	Intron 13 of 31	1	NM_001704.3	ENSP00000359630.1
ADGRB3	ENST00000546190.5	c.2108-11049A>G		intron_variant	Intron 11 of 29	1		ENSP00000441821.2
ADGRB3	ENST00000684661.1	n.2108-11049A>G		intron_variant	Intron 13 of 31			ENSP00000507613.1

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64483 AN: 151768 Hom.: 14372 Cov.: 31

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.0369

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.425 AC: 64509 AN: 151886 Hom.: 14381 Cov.: 31 AF XY: 0.421 AC XY: 31267 AN XY: 74216

African (AFR) AF: 0.469 AC: 19418 AN: 41408

American (AMR) AF: 0.317 AC: 4831 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1975 AN: 3470

East Asian (EAS) AF: 0.0370 AC: 191 AN: 5166

South Asian (SAS) AF: 0.315 AC: 1519 AN: 4818

European-Finnish (FIN) AF: 0.456 AC: 4811 AN: 10540

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.448 AC: 30416 AN: 67924

Other (OTH) AF: 0.417 AC: 882 AN: 2114

Alfa AF: 0.419 Hom.: 2402

Bravo AF: 0.415

Asia WGS AF: 0.171 AC: 595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.67
DANN	Benign	0.44
PhyloP100		-0.44
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: rs7743332; hg19: chr6-69747028;