Variant chr6-142367690-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_198569.3(ADGRG6):c.225C>T(p.Thr75=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00743 in 1,613,694 control chromosomes in the GnomAD database, including 431 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.026 ( 148 hom., cov: 32)

Exomes 𝑓: 0.0055 ( 283 hom. )

Consequence

ADGRG6
NM_198569.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.12

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 -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 6-142367690-C-T is Benign according to our data. Variant chr6-142367690-C-T is described in ClinVar as [Benign]. Clinvar id is 1243331.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-3.12 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0786 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.225C>T	p.Thr75=	synonymous_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.225C>T	p.Thr75=	synonymous_variant	3/25	1	NM_198569.3	ENSP00000356581		Q86SQ4-3

Frequencies

GnomAD3 genomes

AF:

0.0262

AC:

3982

AN:

152024

Hom.:

147

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0807

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0124

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.0583

Gnomad SAS

AF:

0.00581

Gnomad FIN

AF:

0.000189

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000985

Gnomad OTH

AF:

0.0216

GnomAD3 exomes

AF:

0.0105

AC:

2615

AN:

249118

Hom.:

AF XY:

0.00895

AC XY:

1210

AN XY:

135140

show subpopulations

Gnomad AFR exome

AF:

0.0809

Gnomad AMR exome

AF:

0.00624

Gnomad ASJ exome

AF:

0.00249

Gnomad EAS exome

AF:

0.0485

Gnomad SAS exome

AF:

0.00294

Gnomad FIN exome

AF:

0.0000928

Gnomad NFE exome

AF:

0.00101

Gnomad OTH exome

AF:

0.00744

GnomAD4 exome

AF:

0.00547

AC:

7989

AN:

1461552

Hom.:

283

Cov.:

AF XY:

0.00530

AC XY:

3850

AN XY:

727062

show subpopulations

Gnomad4 AFR exome

AF:

0.0861

Gnomad4 AMR exome

AF:

0.00660

Gnomad4 ASJ exome

AF:

0.00210

Gnomad4 EAS exome

AF:

0.0775

Gnomad4 SAS exome

AF:

0.00318

Gnomad4 FIN exome

AF:

0.0000562

Gnomad4 NFE exome

AF:

0.000679

Gnomad4 OTH exome

AF:

0.00994

GnomAD4 genome

AF:

0.0263

AC:

3998

AN:

152142

Hom.:

148

Cov.:

AF XY:

0.0252

AC XY:

1876

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.0809

Gnomad4 AMR

AF:

0.0124

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.0587

Gnomad4 SAS

AF:

0.00561

Gnomad4 FIN

AF:

0.000189

Gnomad4 NFE

AF:

0.000985

Gnomad4 OTH

AF:

0.0213

Alfa

AF:

0.0137

Hom.:

Bravo

AF:

0.0302

Asia WGS

AF:

0.0330

AC:

115

AN:

3478

EpiCase

AF:

0.00142

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

GeneDx

May 04, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

0.85

DANN

Benign

0.67

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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