rs779475

Positions:

• chr6-69213436-A-T

Variant summary

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

The NM_001704.3(ADGRB3):​c.2481-19854A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,082 control chromosomes in the GnomAD database, including 12,300 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 0.38 (12300 hom., cov: 32)
• Consequence: ADGRB3 NM_001704.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADGRB3	NM_001704.3	c.2481-19854A>T		intron_variant		ENST00000370598.6	NP_001695.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADGRB3	ENST00000370598.6	c.2481-19854A>T		intron_variant		1	NM_001704.3	ENSP00000359630	P1
ADGRB3	ENST00000546190.5	c.2481-19854A>T		intron_variant		1		ENSP00000441821	P1
ADGRB3	ENST00000684661.1	c.2481-19854A>T		intron_variant, NMD_transcript_variant				ENSP00000507613

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58385 AN: 151964 Hom.: 12278 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.384 AC: 58449 AN: 152082 Hom.: 12300 Cov.: 32 AF XY: 0.375 AC XY: 27896 AN XY: 74348

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.374

Alfa AF: 0.372 Hom.: 1393

Bravo AF: 0.403

Asia WGS AF: 0.179 AC: 622 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.72
DANN	Benign	0.61

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: rs779475; hg19: chr6-69923328;