rs10485436

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.15
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ADGRB3NM_001704.3 linkuse as main transcriptc.758-25283A>G intron_variant ENST00000370598.6 NP_001695.2 O60242-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ADGRB3ENST00000370598.6 linkuse as main transcriptc.758-25283A>G intron_variant 1 NM_001704.3 ENSP00000359630.1 O60242-1
ADGRB3ENST00000546190.5 linkuse as main transcriptc.758-25283A>G intron_variant 1 ENSP00000441821.2 O60242-1
ADGRB3ENST00000684661.1 linkuse as main transcriptn.758-25283A>G intron_variant ENSP00000507613.1 A0A804HJR2

Frequencies

GnomAD3 genomes
AF:
0.0998
AC:
15184
AN:
152122
Hom.:
839
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.0523
Gnomad4 AMR
AF:
0.0995
Gnomad4 ASJ
AF:
0.122
Gnomad4 EAS
AF:
0.0931
Gnomad4 SAS
AF:
0.0823
Gnomad4 FIN
AF:
0.120
Gnomad4 NFE
AF:
0.125
Gnomad4 OTH
AF:
0.118
Alfa
AF:
0.118
Hom.:
1432
Bravo
AF:
0.0962
Asia WGS
AF:
0.0660
AC:
231
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.042
DANN
Benign
0.23

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10485436; hg19: chr6-69615168; API