rs10485436

Variant names:

• chr6-68905276-A-G
• rs10485436
• NM_001704.3:c.758-25283A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-68905276-A-G
• chr6-68905276-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001704.3(ADGRB3):​c.758-25283A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0997 in 152,240 control chromosomes in the GnomAD database, including 839 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 0.10 (839 hom., cov: 32)
• Consequence: ADGRB3 NM_001704.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 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.758-25283A>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.758-25283A>G		intron	N/A	ENSP00000359630.1	O60242-1
	ADGRB3	ENST00000546190.5	TSL:1	c.758-25283A>G		intron	N/A	ENSP00000441821.2	O60242-1
	ADGRB3	ENST00000684661.1		n.758-25283A>G		intron	N/A	ENSP00000507613.1	A0A804HJR2

Frequencies

GnomAD3 genomes AF: 0.0998 AC: 15184 AN: 152122 Hom.: 839 Cov.: 32

Gnomad AFR AF: 0.0524

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0997

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.0930

Gnomad SAS AF: 0.0823

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.0997 AC: 15175 AN: 152240 Hom.: 839 Cov.: 32 AF XY: 0.101 AC XY: 7514 AN XY: 74424

African (AFR) AF: 0.0523 AC: 2173 AN: 41578

American (AMR) AF: 0.0995 AC: 1520 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 422 AN: 3466

East Asian (EAS) AF: 0.0931 AC: 482 AN: 5180

South Asian (SAS) AF: 0.0823 AC: 397 AN: 4822

European-Finnish (FIN) AF: 0.120 AC: 1268 AN: 10604

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8531 AN: 67998

Other (OTH) AF: 0.118 AC: 250 AN: 2110

Alfa AF: 0.115 Hom.: 1885

Bravo AF: 0.0962

Asia WGS AF: 0.0660 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.042
DANN	Benign	0.23
PhyloP100		-2.1
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: rs10485436; hg19: chr6-69615168;