NM_001704.3:c.2107+7902C>T

Variant names:

• chr6-69026401-C-T
• rs1889878
• NM_001704.3:c.2107+7902C>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.2107+7902C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 151,840 control chromosomes in the GnomAD database, including 14,358 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 0.42 (14358 hom., cov: 31)
• Consequence: ADGRB3 NM_001704.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.463 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.2107+7902C>T		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.2107+7902C>T		intron	N/A	ENSP00000359630.1
	ADGRB3	ENST00000546190.5	TSL:1	c.2107+7902C>T		intron	N/A	ENSP00000441821.2
	ADGRB3	ENST00000684661.1		n.2107+7902C>T		intron	N/A	ENSP00000507613.1

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64427 AN: 151722 Hom.: 14349 Cov.: 31

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.0367

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.424 AC: 64453 AN: 151840 Hom.: 14358 Cov.: 31 AF XY: 0.421 AC XY: 31245 AN XY: 74208

African (AFR) AF: 0.469 AC: 19408 AN: 41396

American (AMR) AF: 0.316 AC: 4814 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1970 AN: 3464

East Asian (EAS) AF: 0.0368 AC: 190 AN: 5168

South Asian (SAS) AF: 0.315 AC: 1512 AN: 4794

European-Finnish (FIN) AF: 0.457 AC: 4813 AN: 10526

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.448 AC: 30402 AN: 67922

Other (OTH) AF: 0.416 AC: 880 AN: 2114

Alfa AF: 0.412 Hom.: 5268

Bravo AF: 0.414

Asia WGS AF: 0.171 AC: 596 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	0.72
DANN	Benign	0.29
PhyloP100		-0.35
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: rs1889878; hg19: chr6-69736293;