rs10485435

Variant names:

• chr6-68905723-G-T
• rs10485435
• NM_001704.3:c.758-24836G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001704.3(ADGRB3):​c.758-24836G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,972 control chromosomes in the GnomAD database, including 8,261 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 0.33 (8261 hom., cov: 32)
• Consequence: ADGRB3 NM_001704.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 8 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRB3	NM_001704.3	c.758-24836G>T		intron_variant	Intron 3 of 31	ENST00000370598.6	NP_001695.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRB3	ENST00000370598.6	c.758-24836G>T		intron_variant	Intron 3 of 31	1	NM_001704.3	ENSP00000359630.1
ADGRB3	ENST00000546190.5	c.758-24836G>T		intron_variant	Intron 1 of 29	1		ENSP00000441821.2
ADGRB3	ENST00000684661.1	n.758-24836G>T		intron_variant	Intron 3 of 31			ENSP00000507613.1

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49847 AN: 151852 Hom.: 8247 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.328 AC: 49888 AN: 151972 Hom.: 8261 Cov.: 32 AF XY: 0.328 AC XY: 24371 AN XY: 74254

African (AFR) AF: 0.374 AC: 15493 AN: 41462

American (AMR) AF: 0.330 AC: 5030 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 848 AN: 3470

East Asian (EAS) AF: 0.277 AC: 1429 AN: 5152

South Asian (SAS) AF: 0.391 AC: 1879 AN: 4808

European-Finnish (FIN) AF: 0.303 AC: 3197 AN: 10554

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20952 AN: 67962

Other (OTH) AF: 0.300 AC: 634 AN: 2110

Alfa AF: 0.313 Hom.: 29135

Bravo AF: 0.328

Asia WGS AF: 0.363 AC: 1261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	16
DANN	Benign	0.85
PhyloP100		1.1
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: rs10485435; hg19: chr6-69615615;