rs10485428

chr6-69061272-T-C

Variant summary

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

The NM_001704.3(ADGRB3):c.2334-1662T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0606 in 151,876 control chromosomes in the GnomAD database, including 354 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 0.061 (354 hom., cov: 32)
• Consequence: ADGRB3 NM_001704.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.743

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADGRB3	NM_001704.3	c.2334-1662T>C		intron_variant		ENST00000370598.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADGRB3	ENST00000370598.6	c.2334-1662T>C		intron_variant		1	NM_001704.3	P1
ADGRB3	ENST00000546190.5	c.2334-1662T>C		intron_variant		1		P1
ADGRB3	ENST00000684661.1	c.2334-1662T>C		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0607 AC: 9210 AN: 151758 Hom.: 353 Cov.: 32

Gnomad AFR AF: 0.0165

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0562

Gnomad ASJ AF: 0.0184

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0853

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0882

Gnomad OTH AF: 0.0547

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

GnomAD4 genome AF: 0.0606 AC: 9205 AN: 151876 Hom.: 354 Cov.: 32 AF XY: 0.0619 AC XY: 4598 AN XY: 74230

Gnomad4 AFR AF: 0.0165

Gnomad4 AMR AF: 0.0558

Gnomad4 ASJ AF: 0.0184

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0864

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0882

Gnomad4 OTH AF: 0.0532

Alfa AF: 0.0816 Hom.: 264

Bravo AF: 0.0526

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.1
Dann	Benign	0.40

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: rs10485428; hg19: chr6-69771164;