Variant rs6924002 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000310357.8(GPRC6A):c.1863A>T(p.Thr621=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 1,613,426 control chromosomes in the GnomAD database, including 82,765 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 0.30 ( 7271 hom., cov: 33)

Exomes 𝑓: 0.32 ( 75494 hom. )

Consequence

GPRC6A
ENST00000310357.8 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.76

Variant links:

Genes affected

GPRC6A (HGNC:18510): (G protein-coupled receptor class C group 6 member A) Members of family C of the G protein-coupled receptor (GPCR) superfamily, such as GPRC6A, are characterized by an evolutionarily conserved amino acid-sensing motif linked to an intramembranous 7-transmembrane loop region. Several members of GPCR family C, including GPRC6A, also have a long N-terminal domain (summary by Pi et al., 2005 [PubMed 16199532]).[supplied by OMIM, Nov 2010]

GPRC6A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP7

Synonymous conserved (PhyloP=-1.76 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
GPRC6A	NM_148963.4 linkuse as main transcript	c.1863A>T	p.Thr621=	synonymous_variant	6/6	ENST00000310357.8	NP_683766.2
GPRC6A	NM_001286355.1 linkuse as main transcript	c.1650A>T	p.Thr550=	synonymous_variant	5/5		NP_001273284.1
GPRC6A	NM_001286354.1 linkuse as main transcript	c.1338A>T	p.Thr446=	synonymous_variant	6/6		NP_001273283.1
GPRC6A	XM_017010475.2 linkuse as main transcript	c.1722A>T	p.Thr574=	synonymous_variant	7/7		XP_016865964.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPRC6A	ENST00000310357.8 linkuse as main transcript	c.1863A>T	p.Thr621=	synonymous_variant	6/6	1	NM_148963.4	ENSP00000309493	P1	Q5T6X5-1
GPRC6A	ENST00000368549.7 linkuse as main transcript	c.1650A>T	p.Thr550=	synonymous_variant	5/5	1		ENSP00000357537		Q5T6X5-3
GPRC6A	ENST00000530250.1 linkuse as main transcript	c.1338A>T	p.Thr446=	synonymous_variant	6/6	1		ENSP00000433465		Q5T6X5-2

Frequencies

GnomAD3 genomes

AF:

0.299

AC:

45379

AN:

151986

Hom.:

7281

Cov.:

show subpopulations

Gnomad AFR

AF:

0.215

Gnomad AMI

AF:

0.451

Gnomad AMR

AF:

0.338

Gnomad ASJ

AF:

0.479

Gnomad EAS

AF:

0.527

Gnomad SAS

AF:

0.266

Gnomad FIN

AF:

0.257

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.318

Gnomad OTH

AF:

0.346

GnomAD3 exomes

AF:

0.325

AC:

81565

AN:

250672

Hom.:

14191

AF XY:

0.324

AC XY:

43915

AN XY:

135474

show subpopulations

Gnomad AFR exome

AF:

0.210

Gnomad AMR exome

AF:

0.327

Gnomad ASJ exome

AF:

0.478

Gnomad EAS exome

AF:

0.547

Gnomad SAS exome

AF:

0.261

Gnomad FIN exome

AF:

0.259

Gnomad NFE exome

AF:

0.321

Gnomad OTH exome

AF:

0.337

GnomAD4 exome

AF:

0.317

AC:

463011

AN:

1461322

Hom.:

75494

Cov.:

AF XY:

0.316

AC XY:

229967

AN XY:

726974

show subpopulations

Gnomad4 AFR exome

AF:

0.219

Gnomad4 AMR exome

AF:

0.328

Gnomad4 ASJ exome

AF:

0.475

Gnomad4 EAS exome

AF:

0.521

Gnomad4 SAS exome

AF:

0.261

Gnomad4 FIN exome

AF:

0.264

Gnomad4 NFE exome

AF:

0.313

Gnomad4 OTH exome

AF:

0.342

GnomAD4 genome

AF:

0.298

AC:

45377

AN:

152104

Hom.:

7271

Cov.:

AF XY:

0.297

AC XY:

22085

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.215

Gnomad4 AMR

AF:

0.337

Gnomad4 ASJ

AF:

0.479

Gnomad4 EAS

AF:

0.527

Gnomad4 SAS

AF:

0.265

Gnomad4 FIN

AF:

0.257

Gnomad4 NFE

AF:

0.318

Gnomad4 OTH

AF:

0.345

Alfa

AF:

0.329

Hom.:

2824

Bravo

AF:

0.305

Asia WGS

AF:

0.371

AC:

1289

AN:

3478

EpiCase

AF:

0.339

EpiControl

AF:

0.330

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.79

DANN

Benign

0.62

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over