Variant rs9937918 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001304376.3(ADGRG5):c.846C>T(p.Arg282=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 1,610,494 control chromosomes in the GnomAD database, including 86,127 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.34 ( 9556 hom., cov: 32)

Exomes 𝑓: 0.31 ( 76571 hom. )

Consequence

ADGRG5
NM_001304376.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.27

Variant links:

Genes affected

ADGRG5 (HGNC:19010): (adhesion G protein-coupled receptor G5) This gene encodes a member of the adhesion family of G-protein coupled receptors. Members of this family are characterized by long N-termini and multiple functional domains. They may play a role in the immune system as well as in the central nervous system. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ADGRG5 links:

LOC105371291 (HGNC:):

LOC105371291 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP7

Synonymous conserved (PhyloP=-3.27 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADGRG5	NM_001304376.3 linkuse as main transcript	c.846C>T	p.Arg282=	synonymous_variant	9/12	ENST00000349457.8	NP_001291305.1
LOC105371291	XR_933627.4 linkuse as main transcript	n.587-31G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
ADGRG5	ENST00000349457.8 linkuse as main transcript	c.846C>T	p.Arg282=	synonymous_variant	9/12	1	NM_001304376.3	ENSP00000290823	P1
ADGRG5	ENST00000340339.4 linkuse as main transcript	c.846C>T	p.Arg282=	synonymous_variant	9/12	1		ENSP00000342981	P1
ADGRG5	ENST00000394361.8 linkuse as main transcript	n.932C>T		non_coding_transcript_exon_variant	9/11	2
ADGRG5	ENST00000564607.1 linkuse as main transcript	n.2379C>T		non_coding_transcript_exon_variant	8/11	2

Frequencies

GnomAD3 genomes

AF:

0.341

AC:

51844

AN:

151848

Hom.:

9537

Cov.:

show subpopulations

Gnomad AFR

AF:

0.369

Gnomad AMI

AF:

0.251

Gnomad AMR

AF:

0.446

Gnomad ASJ

AF:

0.321

Gnomad EAS

AF:

0.708

Gnomad SAS

AF:

0.408

Gnomad FIN

AF:

0.297

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.278

Gnomad OTH

AF:

0.339

GnomAD3 exomes

AF:

0.376

AC:

92964

AN:

247470

Hom.:

19896

AF XY:

0.365

AC XY:

48889

AN XY:

133960

show subpopulations

Gnomad AFR exome

AF:

0.369

Gnomad AMR exome

AF:

0.565

Gnomad ASJ exome

AF:

0.324

Gnomad EAS exome

AF:

0.705

Gnomad SAS exome

AF:

0.394

Gnomad FIN exome

AF:

0.299

Gnomad NFE exome

AF:

0.281

Gnomad OTH exome

AF:

0.340

GnomAD4 exome

AF:

0.309

AC:

450233

AN:

1458528

Hom.:

76571

Cov.:

AF XY:

0.310

AC XY:

225004

AN XY:

725662

show subpopulations

Gnomad4 AFR exome

AF:

0.375

Gnomad4 AMR exome

AF:

0.551

Gnomad4 ASJ exome

AF:

0.314

Gnomad4 EAS exome

AF:

0.746

Gnomad4 SAS exome

AF:

0.391

Gnomad4 FIN exome

AF:

0.301

Gnomad4 NFE exome

AF:

0.274

Gnomad4 OTH exome

AF:

0.328

GnomAD4 genome

AF:

0.342

AC:

51908

AN:

151966

Hom.:

9556

Cov.:

AF XY:

0.348

AC XY:

25829

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.370

Gnomad4 AMR

AF:

0.446

Gnomad4 ASJ

AF:

0.321

Gnomad4 EAS

AF:

0.708

Gnomad4 SAS

AF:

0.407

Gnomad4 FIN

AF:

0.297

Gnomad4 NFE

AF:

0.278

Gnomad4 OTH

AF:

0.341

Alfa

AF:

0.298

Hom.:

13422

Bravo

AF:

0.355

Asia WGS

AF:

0.564

AC:

1962

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

3.6

DANN

Benign

0.57

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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