Variant 1-31727462-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2

The NM_001364857.2(ADGRB2):c.4716G>A(p.Glu1572=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00496 in 1,590,850 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0044 ( 7 hom., cov: 32)

Exomes 𝑓: 0.0050 ( 38 hom. )

Consequence

ADGRB2
NM_001364857.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.185

Variant links:

Genes affected

ADGRB2 (HGNC:944): (adhesion G protein-coupled receptor B2) This gene encodes a a seven-span transmembrane protein that is thought to be a member of the secretin receptor family. The encoded protein is a brain-specific inhibitor of angiogenesis. The mature peptide may be further cleaved into additional products (PMID:20367554). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]

ADGRB2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP6

Variant 1-31727462-C-T is Benign according to our data. Variant chr1-31727462-C-T is described in ClinVar as [Benign]. Clinvar id is 773632.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.185 with no splicing effect.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00442 (673/152298) while in subpopulation EAS AF= 0.0343 (178/5184). AF 95% confidence interval is 0.0302. There are 7 homozygotes in gnomad4. There are 309 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADGRB2	NM_001364857.2 linkuse as main transcript	c.4716G>A	p.Glu1572=	synonymous_variant	33/33	ENST00000373658.8	NP_001351786.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADGRB2	ENST00000373658.8 linkuse as main transcript	c.4716G>A	p.Glu1572=	synonymous_variant	33/33	5	NM_001364857.2	ENSP00000362762		O60241-1

Frequencies

GnomAD3 genomes

AF:

0.00442

AC:

672

AN:

152180

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000772

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00229

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.0343

Gnomad SAS

AF:

0.00186

Gnomad FIN

AF:

0.00480

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00513

Gnomad OTH

AF:

0.00621

GnomAD3 exomes

AF:

0.00611

AC:

1382

AN:

226298

Hom.:

AF XY:

0.00597

AC XY:

736

AN XY:

123204

show subpopulations

Gnomad AFR exome

AF:

0.000654

Gnomad AMR exome

AF:

0.000520

Gnomad ASJ exome

AF:

0.000453

Gnomad EAS exome

AF:

0.0348

Gnomad SAS exome

AF:

0.00187

Gnomad FIN exome

AF:

0.00561

Gnomad NFE exome

AF:

0.00575

Gnomad OTH exome

AF:

0.00388

GnomAD4 exome

AF:

0.00502

AC:

7218

AN:

1438552

Hom.:

Cov.:

AF XY:

0.00488

AC XY:

3492

AN XY:

715804

show subpopulations

Gnomad4 AFR exome

AF:

0.000727

Gnomad4 AMR exome

AF:

0.000817

Gnomad4 ASJ exome

AF:

0.000399

Gnomad4 EAS exome

AF:

0.0200

Gnomad4 SAS exome

AF:

0.00151

Gnomad4 FIN exome

AF:

0.00531

Gnomad4 NFE exome

AF:

0.00508

Gnomad4 OTH exome

AF:

0.00595

GnomAD4 genome

AF:

0.00442

AC:

673

AN:

152298

Hom.:

Cov.:

AF XY:

0.00415

AC XY:

309

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.000770

Gnomad4 AMR

AF:

0.00229

Gnomad4 ASJ

AF:

0.000865

Gnomad4 EAS

AF:

0.0343

Gnomad4 SAS

AF:

0.00187

Gnomad4 FIN

AF:

0.00480

Gnomad4 NFE

AF:

0.00513

Gnomad4 OTH

AF:

0.00662

Alfa

AF:

0.00447

Hom.:

Bravo

AF:

0.00396

Asia WGS

AF:

0.0130

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 18, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

6.6

DANN

Benign

0.53

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over