6-68990868-T-G

Variant names:

• chr6-68990868-T-G
• rs3798995
• NM_001704.3:c.1735-2900T>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.1735-2900T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,124 control chromosomes in the GnomAD database, including 1,669 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 0.11 (1669 hom., cov: 32)
• Consequence: ADGRB3 NM_001704.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.801
• 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=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 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.1735-2900T>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.1735-2900T>G		intron	N/A	ENSP00000359630.1	O60242-1
	ADGRB3	ENST00000546190.5	TSL:1	c.1735-2900T>G		intron	N/A	ENSP00000441821.2	O60242-1
	ADGRB3	ENST00000684661.1		n.1735-2900T>G		intron	N/A	ENSP00000507613.1	A0A804HJR2

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16218 AN: 152006 Hom.: 1661 Cov.: 32

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0864

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.107 AC: 16245 AN: 152124 Hom.: 1669 Cov.: 32 AF XY: 0.113 AC XY: 8378 AN XY: 74368

African (AFR) AF: 0.0438 AC: 1820 AN: 41546

American (AMR) AF: 0.166 AC: 2540 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0680 AC: 236 AN: 3472

East Asian (EAS) AF: 0.565 AC: 2899 AN: 5132

South Asian (SAS) AF: 0.198 AC: 954 AN: 4820

European-Finnish (FIN) AF: 0.128 AC: 1351 AN: 10582

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0864 AC: 5875 AN: 67986

Other (OTH) AF: 0.136 AC: 288 AN: 2116

Alfa AF: 0.104 Hom.: 191

Bravo AF: 0.109

Asia WGS AF: 0.396 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	15
DANN	Benign	0.86
PhyloP100		0.80
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: rs3798995; hg19: chr6-69700760;