6-69061272-T-C

Variant names:

• chr6-69061272-T-C
• rs10485428
• NM_001704.3:c.2334-1662T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0863 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRB3	NM_001704.3	MANE Select	c.2334-1662T>C		intron	N/A	NP_001695.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRB3	ENST00000370598.6	TSL:1 MANE Select	c.2334-1662T>C		intron	N/A	ENSP00000359630.1
	ADGRB3	ENST00000546190.5	TSL:1	c.2334-1662T>C		intron	N/A	ENSP00000441821.2
	ADGRB3	ENST00000684661.1		n.2334-1662T>C		intron	N/A	ENSP00000507613.1

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

African (AFR) AF: 0.0165 AC: 683 AN: 41468

American (AMR) AF: 0.0558 AC: 848 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.0184 AC: 64 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5182

South Asian (SAS) AF: 0.0864 AC: 416 AN: 4816

European-Finnish (FIN) AF: 0.101 AC: 1066 AN: 10568

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0882 AC: 5986 AN: 67874

Other (OTH) AF: 0.0532 AC: 112 AN: 2106

Alfa AF: 0.0818 Hom.: 297

Bravo AF: 0.0526

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.40
PhyloP100		-0.74
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: rs10485428; hg19: chr6-69771164;