Variant rs1144122 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_032787.3(ADGRG7):c.451A>G(p.Lys151Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 1,609,822 control chromosomes in the GnomAD database, including 83,691 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.26 ( 5806 hom., cov: 32)

Exomes 𝑓: 0.32 ( 77885 hom. )

Consequence

ADGRG7
NM_032787.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.96

Variant links:

Genes affected

ADGRG7 (HGNC:19241): (adhesion G protein-coupled receptor G7) Predicted to enable G protein-coupled receptor activity. Predicted to be involved in adenylate cyclase-activating G protein-coupled receptor signaling pathway. Predicted to be integral component of membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ADGRG7 links:

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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 (MetaRNN=0.0015993416).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ADGRG7	NM_032787.3 linkuse as main transcript	c.451A>G	p.Lys151Glu	missense_variant	5/16	ENST00000273352.8	NP_116176.2
ADGRG7	XM_047449088.1 linkuse as main transcript	c.46A>G	p.Lys16Glu	missense_variant	3/14		XP_047305044.1
ADGRG7	NM_001308362.1 linkuse as main transcript	c.-187A>G		5_prime_UTR_variant	1/10		NP_001295291.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
ADGRG7	ENST00000273352.8 linkuse as main transcript	c.451A>G	p.Lys151Glu	missense_variant	5/16	1	NM_032787.3	ENSP00000273352	P1
ADGRG7	ENST00000475887.1 linkuse as main transcript	c.-187A>G		5_prime_UTR_variant	1/10	2		ENSP00000419788
ADGRG7	ENST00000481361.1 linkuse as main transcript	n.143A>G		non_coding_transcript_exon_variant	1/4	4
ADGRG7	ENST00000493081.1 linkuse as main transcript	n.141A>G		non_coding_transcript_exon_variant	1/2	4

Frequencies

GnomAD3 genomes

AF:

0.259

AC:

39361

AN:

151856

Hom.:

5813

Cov.:

show subpopulations

Gnomad AFR

AF:

0.162

Gnomad AMI

AF:

0.377

Gnomad AMR

AF:

0.214

Gnomad ASJ

AF:

0.385

Gnomad EAS

AF:

0.0133

Gnomad SAS

AF:

0.149

Gnomad FIN

AF:

0.297

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.341

Gnomad OTH

AF:

0.275

GnomAD3 exomes

AF:

0.255

AC:

63484

AN:

248896

Hom.:

9651

AF XY:

0.260

AC XY:

34966

AN XY:

134412

show subpopulations

Gnomad AFR exome

AF:

0.160

Gnomad AMR exome

AF:

0.151

Gnomad ASJ exome

AF:

0.371

Gnomad EAS exome

AF:

0.0109

Gnomad SAS exome

AF:

0.160

Gnomad FIN exome

AF:

0.300

Gnomad NFE exome

AF:

0.344

Gnomad OTH exome

AF:

0.286

GnomAD4 exome

AF:

0.315

AC:

459497

AN:

1457848

Hom.:

77885

Cov.:

AF XY:

0.312

AC XY:

226350

AN XY:

725094

show subpopulations

Gnomad4 AFR exome

AF:

0.154

Gnomad4 AMR exome

AF:

0.160

Gnomad4 ASJ exome

AF:

0.375

Gnomad4 EAS exome

AF:

0.00794

Gnomad4 SAS exome

AF:

0.163

Gnomad4 FIN exome

AF:

0.301

Gnomad4 NFE exome

AF:

0.349

Gnomad4 OTH exome

AF:

0.302

GnomAD4 genome

AF:

0.259

AC:

39357

AN:

151974

Hom.:

5806

Cov.:

AF XY:

0.254

AC XY:

18835

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.161

Gnomad4 AMR

AF:

0.213

Gnomad4 ASJ

AF:

0.385

Gnomad4 EAS

AF:

0.0133

Gnomad4 SAS

AF:

0.148

Gnomad4 FIN

AF:

0.297

Gnomad4 NFE

AF:

0.341

Gnomad4 OTH

AF:

0.270

Alfa

AF:

0.319

Hom.:

19063

Bravo

AF:

0.251

TwinsUK

AF:

0.369

AC:

1369

ALSPAC

AF:

0.361

AC:

1392

ESP6500AA

AF:

0.167

AC:

738

ESP6500EA

AF:

0.343

AC:

2954

ExAC

AF:

0.256

AC:

31050

Asia WGS

AF:

0.0910

AC:

320

AN:

3478

EpiCase

AF:

0.349

EpiControl

AF:

0.349

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.059

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.0060

DANN

Benign

0.56

DEOGEN2

Benign

0.0016

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.0088

LIST_S2

Benign

0.27

MetaRNN

Benign

0.0016

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.31

PROVEAN

Benign

0.83

REVEL

Benign

0.014

Sift

Benign

0.95

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.0060

MPC

0.077

ClinPred

0.0017

GERP RS

-1.4

Varity_R

0.032

gMVP

0.27

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over