rs314218

chr6-69145805-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001704.3(ADGRB3):c.2480+69767C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 151,720 control chromosomes in the GnomAD database, including 2,124 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 0.16 (2124 hom., cov: 30)
• Consequence: ADGRB3 NM_001704.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206

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

Verdict is Benign. Variant got -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 = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADGRB3	NM_001704.3	c.2480+69767C>T		intron_variant		ENST00000370598.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADGRB3	ENST00000370598.6	c.2480+69767C>T		intron_variant		1	NM_001704.3	P1
ADGRB3	ENST00000546190.5	c.2480+69767C>T		intron_variant		1		P1
ADGRB3	ENST00000684661.1	c.2480+69767C>T		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24113 AN: 151600 Hom.: 2119 Cov.: 30

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.00137

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.159 AC: 24124 AN: 151720 Hom.: 2124 Cov.: 30 AF XY: 0.155 AC XY: 11498 AN XY: 74132

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.00137

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.144

Alfa AF: 0.160 Hom.: 242

Bravo AF: 0.157

Asia WGS AF: 0.0580 AC: 203 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	2.7
Dann	Benign	0.39

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: rs314218; hg19: chr6-69855697;