Variant chr6-142367832-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_198569.3(ADGRG6):c.367A>G(p.Ser123Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0271 in 1,613,664 control chromosomes in the GnomAD database, including 756 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.024 ( 59 hom., cov: 32)

Exomes 𝑓: 0.027 ( 697 hom. )

Consequence

ADGRG6
NM_198569.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 7.03

Variant links:

Genes affected

ADGRG6 (HGNC:13841): (adhesion G protein-coupled receptor G6) This gene, which is upregulated in human umbilical vein endothelial cells, encodes a G protein-coupled receptor. Variations in this gene can affect a person's stature. Multiple transcript variants encoding different proteins have been found for this gene. [provided by RefSeq, Mar 2009]

ADGRG6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 6-142367832-A-G is Benign according to our data. Variant chr6-142367832-A-G is described in ClinVar as [Benign]. Clinvar id is 1277289.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADGRG6	NM_198569.3 linkuse as main transcript	c.367A>G	p.Ser123Gly	missense_variant	3/25	ENST00000367609.8	NP_940971.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADGRG6	ENST00000367609.8 linkuse as main transcript	c.367A>G	p.Ser123Gly	missense_variant	3/25	1	NM_198569.3	ENSP00000356581		Q86SQ4-3

Frequencies

GnomAD3 genomes

AF:

0.0241

AC:

3669

AN:

152210

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00579

Gnomad AMI

AF:

0.0417

Gnomad AMR

AF:

0.0618

Gnomad ASJ

AF:

0.0144

Gnomad EAS

AF:

0.0252

Gnomad SAS

AF:

0.0153

Gnomad FIN

AF:

0.0184

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0284

Gnomad OTH

AF:

0.0277

GnomAD3 exomes

AF:

0.0304

AC:

7551

AN:

248690

Hom.:

182

AF XY:

0.0285

AC XY:

3845

AN XY:

134894

show subpopulations

Gnomad AFR exome

AF:

0.00523

Gnomad AMR exome

AF:

0.0749

Gnomad ASJ exome

AF:

0.0175

Gnomad EAS exome

AF:

0.0234

Gnomad SAS exome

AF:

0.0175

Gnomad FIN exome

AF:

0.0194

Gnomad NFE exome

AF:

0.0281

Gnomad OTH exome

AF:

0.0291

GnomAD4 exome

AF:

0.0274

AC:

40109

AN:

1461336

Hom.:

697

Cov.:

AF XY:

0.0268

AC XY:

19495

AN XY:

726980

show subpopulations

Gnomad4 AFR exome

AF:

0.00430

Gnomad4 AMR exome

AF:

0.0728

Gnomad4 ASJ exome

AF:

0.0179

Gnomad4 EAS exome

AF:

0.0278

Gnomad4 SAS exome

AF:

0.0174

Gnomad4 FIN exome

AF:

0.0190

Gnomad4 NFE exome

AF:

0.0279

Gnomad4 OTH exome

AF:

0.0254

GnomAD4 genome

AF:

0.0241

AC:

3678

AN:

152328

Hom.:

Cov.:

AF XY:

0.0245

AC XY:

1822

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.00577

Gnomad4 AMR

AF:

0.0622

Gnomad4 ASJ

AF:

0.0144

Gnomad4 EAS

AF:

0.0255

Gnomad4 SAS

AF:

0.0153

Gnomad4 FIN

AF:

0.0184

Gnomad4 NFE

AF:

0.0284

Gnomad4 OTH

AF:

0.0274

Alfa

AF:

0.0286

Hom.:

154

Bravo

AF:

0.0263

TwinsUK

AF:

0.0210

AC:

ALSPAC

AF:

0.0301

AC:

116

ESP6500AA

AF:

0.00871

AC:

ESP6500EA

AF:

0.0293

AC:

241

ExAC

AF:

0.0284

AC:

3433

Asia WGS

AF:

0.0220

AC:

AN:

3478

EpiCase

AF:

0.0284

EpiControl

AF:

0.0304

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

GeneDx

May 04, 2021

This variant is associated with the following publications: (PMID: 29026132) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.24

BayesDel_addAF

Benign

-0.50

BayesDel_noAF

Benign

-0.43

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.25

T;.;.;.;T;.

Eigen

Uncertain

0.57

Eigen_PC

Uncertain

0.63

FATHMM_MKL

Uncertain

0.96

LIST_S2

Uncertain

0.92

D;D;D;D;D;D

MetaRNN

Benign

0.0031

T;T;T;T;T;T

MetaSVM

Benign

-1.1

MutationTaster

Benign

0.66

N;N;N;N

PrimateAI

Uncertain

0.49

PROVEAN

Benign

-1.7

N;N;N;N;N;N

REVEL

Benign

0.15

Sift

Uncertain

0.0010

D;D;D;D;D;T

Sift4G

Uncertain

0.0060

.;.;.;.;D;D

Polyphen

0.88

P;P;P;P;P;.

Vest4

0.15

MPC

0.32

ClinPred

0.032

GERP RS

5.9

Varity_R

0.23

gMVP

0.43

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.23

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.23

Position offset: 0

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