Variant chr6-116792598-A-AGG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_148963.4(GPRC6A):c.2324_2325insCC(p.Glu776LeufsTer19) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0892 in 1,612,338 control chromosomes in the GnomAD database, including 10,385 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.16 ( 3332 hom., cov: 33)

Exomes 𝑓: 0.081 ( 7053 hom. )

Consequence

GPRC6A
NM_148963.4 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 7.75

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 -10 ACMG points.

BP6

Variant 6-116792598-A-AGG is Benign according to our data. Variant chr6-116792598-A-AGG is described in ClinVar as [Benign]. Clinvar id is 769689.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.368 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.2324_2325insCC	p.Glu776LeufsTer19	frameshift_variant	6/6	ENST00000310357.8	NP_683766.2
GPRC6A	NM_001286354.1 linkuse as main transcript	c.1799_1800insCC	p.Glu601LeufsTer19	frameshift_variant	6/6		NP_001273283.1
GPRC6A	NM_001286355.1 linkuse as main transcript	c.2111_2112insCC	p.Glu705LeufsTer19	frameshift_variant	5/5		NP_001273284.1
GPRC6A	XM_017010475.2 linkuse as main transcript	c.2183_2184insCC	p.Glu729LeufsTer19	frameshift_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.2324_2325insCC	p.Glu776LeufsTer19	frameshift_variant	6/6	1	NM_148963.4	ENSP00000309493	P1	Q5T6X5-1
GPRC6A	ENST00000368549.7 linkuse as main transcript	c.2111_2112insCC	p.Glu705LeufsTer19	frameshift_variant	5/5	1		ENSP00000357537		Q5T6X5-3
GPRC6A	ENST00000530250.1 linkuse as main transcript	c.1799_1800insCC	p.Glu601LeufsTer19	frameshift_variant	6/6	1		ENSP00000433465		Q5T6X5-2

Frequencies

GnomAD3 genomes

AF:

0.164

AC:

24977

AN:

152008

Hom.:

3321

Cov.:

show subpopulations

Gnomad AFR

AF:

0.373

Gnomad AMI

AF:

0.0868

Gnomad AMR

AF:

0.163

Gnomad ASJ

AF:

0.106

Gnomad EAS

AF:

0.00905

Gnomad SAS

AF:

0.0652

Gnomad FIN

AF:

0.115

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0694

Gnomad OTH

AF:

0.150

GnomAD3 exomes

AF:

0.0493

AC:

10989

AN:

222804

Hom.:

1415

AF XY:

0.0439

AC XY:

5346

AN XY:

121804

show subpopulations

Gnomad AFR exome

AF:

0.233

Gnomad AMR exome

AF:

0.108

Gnomad ASJ exome

AF:

0.0448

Gnomad EAS exome

AF:

0.00214

Gnomad SAS exome

AF:

0.0233

Gnomad FIN exome

AF:

0.0574

Gnomad NFE exome

AF:

0.0287

Gnomad OTH exome

AF:

0.0387

GnomAD4 exome

AF:

0.0814

AC:

118818

AN:

1460212

Hom.:

7053

Cov.:

AF XY:

0.0791

AC XY:

57457

AN XY:

726188

show subpopulations

Gnomad4 AFR exome

AF:

0.374

Gnomad4 AMR exome

AF:

0.207

Gnomad4 ASJ exome

AF:

0.105

Gnomad4 EAS exome

AF:

0.0134

Gnomad4 SAS exome

AF:

0.0608

Gnomad4 FIN exome

AF:

0.110

Gnomad4 NFE exome

AF:

0.0690

Gnomad4 OTH exome

AF:

0.0912

GnomAD4 genome

AF:

0.165

AC:

25032

AN:

152126

Hom.:

3332

Cov.:

AF XY:

0.164

AC XY:

12202

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.373

Gnomad4 AMR

AF:

0.163

Gnomad4 ASJ

AF:

0.106

Gnomad4 EAS

AF:

0.00907

Gnomad4 SAS

AF:

0.0652

Gnomad4 FIN

AF:

0.115

Gnomad4 NFE

AF:

0.0694

Gnomad4 OTH

AF:

0.148

Alfa

AF:

0.0266

Hom.:

Asia WGS

AF:

0.0570

AC:

201

AN:

3478

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

Aug 29, 2018

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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