Variant chr6-142367674-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_198569.3(ADGRG6):c.209C>T(p.Thr70Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00413 in 1,613,586 control chromosomes in the GnomAD database, including 176 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0082 ( 21 hom., cov: 32)

Exomes 𝑓: 0.0037 ( 155 hom. )

Consequence

ADGRG6
NM_198569.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.94

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0047012568).

BP6

Variant 6-142367674-C-T is Benign according to our data. Variant chr6-142367674-C-T is described in ClinVar as [Benign]. Clinvar id is 784098.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0531 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.209C>T	p.Thr70Met	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.209C>T	p.Thr70Met	missense_variant	3/25	1	NM_198569.3	ENSP00000356581		Q86SQ4-3

Frequencies

GnomAD3 genomes

AF:

0.00820

AC:

1246

AN:

151964

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0185

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00485

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.0582

Gnomad SAS

AF:

0.00543

Gnomad FIN

AF:

0.000189

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000823

Gnomad OTH

AF:

0.00577

GnomAD3 exomes

AF:

0.00617

AC:

1537

AN:

249104

Hom.:

AF XY:

0.00574

AC XY:

776

AN XY:

135126

show subpopulations

Gnomad AFR exome

AF:

0.0181

Gnomad AMR exome

AF:

0.00374

Gnomad ASJ exome

AF:

0.00249

Gnomad EAS exome

AF:

0.0485

Gnomad SAS exome

AF:

0.00284

Gnomad FIN exome

AF:

0.000278

Gnomad NFE exome

AF:

0.000992

Gnomad OTH exome

AF:

0.00446

GnomAD4 exome

AF:

0.00371

AC:

5417

AN:

1461506

Hom.:

155

Cov.:

AF XY:

0.00375

AC XY:

2729

AN XY:

727038

show subpopulations

Gnomad4 AFR exome

AF:

0.0187

Gnomad4 AMR exome

AF:

0.00394

Gnomad4 ASJ exome

AF:

0.00210

Gnomad4 EAS exome

AF:

0.0776

Gnomad4 SAS exome

AF:

0.00305

Gnomad4 FIN exome

AF:

0.000187

Gnomad4 NFE exome

AF:

0.000723

Gnomad4 OTH exome

AF:

0.00605

GnomAD4 genome

AF:

0.00822

AC:

1250

AN:

152080

Hom.:

Cov.:

AF XY:

0.00827

AC XY:

615

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.0186

Gnomad4 AMR

AF:

0.00484

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.0585

Gnomad4 SAS

AF:

0.00522

Gnomad4 FIN

AF:

0.000189

Gnomad4 NFE

AF:

0.000823

Gnomad4 OTH

AF:

0.00571

Alfa

AF:

0.00275

Hom.:

Bravo

AF:

0.00956

TwinsUK

AF:

0.000809

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.0168

AC:

ESP6500EA

AF:

0.00121

AC:

ExAC

AF:

0.00622

AC:

752

Asia WGS

AF:

0.0280

AC:

AN:

3478

EpiCase

AF:

0.00147

EpiControl

AF:

0.00107

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

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.49

BayesDel_noAF

Benign

-0.39

CADD

Uncertain

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.26

T;.;.;.;T;.

Eigen

Pathogenic

0.72

Eigen_PC

Pathogenic

0.72

FATHMM_MKL

Uncertain

0.80

LIST_S2

Uncertain

0.96

D;D;D;D;D;D

MetaRNN

Benign

0.0047

T;T;T;T;T;T

MetaSVM

Benign

-0.90

MutationTaster

Benign

0.57

N;N;N;N

PrimateAI

Benign

0.46

PROVEAN

Benign

-1.9

N;N;N;N;N;N

REVEL

Benign

0.22

Sift

Uncertain

0.0010

D;D;D;D;T;T

Sift4G

Uncertain

0.020

.;.;.;.;D;D

Polyphen

1.0

D;D;D;D;D;.

Vest4

0.49

MVP

0.61

MPC

0.54

ClinPred

0.032

GERP RS

6.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.23

gMVP

0.59

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