6-68751549-T-C

Variant names:

• chr6-68751549-T-C
• rs2206836
• NM_001704.3:c.757+112117T>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.757+112117T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,054 control chromosomes in the GnomAD database, including 44,159 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 0.76 (44159 hom., cov: 32)
• Consequence: ADGRB3 NM_001704.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• 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]

ENSG00000308231 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRB3	NM_001704.3	c.757+112117T>C		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.757+112117T>C		intron_variant	Intron 3 of 31	1	NM_001704.3	ENSP00000359630.1

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115457 AN: 151936 Hom.: 44112 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.760 AC: 115563 AN: 152054 Hom.: 44159 Cov.: 32 AF XY: 0.755 AC XY: 56071 AN XY: 74312

African (AFR) AF: 0.756 AC: 31354 AN: 41460

American (AMR) AF: 0.792 AC: 12103 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3007 AN: 3468

East Asian (EAS) AF: 0.868 AC: 4481 AN: 5164

South Asian (SAS) AF: 0.681 AC: 3277 AN: 4810

European-Finnish (FIN) AF: 0.676 AC: 7131 AN: 10554

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.758 AC: 51526 AN: 68006

Other (OTH) AF: 0.807 AC: 1702 AN: 2108

Alfa AF: 0.757 Hom.: 8653

Bravo AF: 0.775

Asia WGS AF: 0.751 AC: 2606 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.86
PhyloP100		-0.20
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: rs2206836; hg19: chr6-69461441;