Variant chr6-116792602-T-TTCC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PM4_SupportingBP6_ModerateBA1

The NM_148963.4(GPRC6A):c.2320_2321insGGA(p.Gly773_Lys774insArg) variant causes a inframe insertion change. The variant allele was found at a frequency of 0.0892 in 1,612,534 control chromosomes in the GnomAD database, including 10,381 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.16 ( 3331 hom., cov: 30)

Exomes 𝑓: 0.081 ( 7050 hom. )

Consequence

GPRC6A
NM_148963.4 inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.95

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 -9 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_148963.4. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant 6-116792602-T-TTCC is Benign according to our data. Variant chr6-116792602-T-TTCC is described in ClinVar as [Benign]. Clinvar id is 769691.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
GPRC6A	NM_148963.4 linkuse as main transcript	c.2320_2321insGGA	p.Gly773_Lys774insArg	inframe_insertion	6/6	ENST00000310357.8
GPRC6A	NM_001286354.1 linkuse as main transcript	c.1795_1796insGGA	p.Gly598_Lys599insArg	inframe_insertion	6/6
GPRC6A	NM_001286355.1 linkuse as main transcript	c.2107_2108insGGA	p.Gly702_Lys703insArg	inframe_insertion	5/5
GPRC6A	XM_017010475.2 linkuse as main transcript	c.2179_2180insGGA	p.Gly726_Lys727insArg	inframe_insertion	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPRC6A	ENST00000310357.8 linkuse as main transcript	c.2320_2321insGGA	p.Gly773_Lys774insArg	inframe_insertion	6/6	1	NM_148963.4	P1	Q5T6X5-1
GPRC6A	ENST00000368549.7 linkuse as main transcript	c.2107_2108insGGA	p.Gly702_Lys703insArg	inframe_insertion	5/5	1			Q5T6X5-3
GPRC6A	ENST00000530250.1 linkuse as main transcript	c.1795_1796insGGA	p.Gly598_Lys599insArg	inframe_insertion	6/6	1			Q5T6X5-2

Frequencies

GnomAD3 genomes

AF:

0.164

AC:

24977

AN:

151988

Hom.:

3320

Cov.:

show subpopulations

Gnomad AFR

AF:

0.373

Gnomad AMI

AF:

0.0868

Gnomad AMR

AF:

0.162

Gnomad ASJ

AF:

0.106

Gnomad EAS

AF:

0.00905

Gnomad SAS

AF:

0.0651

Gnomad FIN

AF:

0.115

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0694

Gnomad OTH

AF:

0.150

GnomAD3 exomes

AF:

0.0464

AC:

10048

AN:

216582

Hom.:

1400

AF XY:

0.0409

AC XY:

4863

AN XY:

118772

show subpopulations

Gnomad AFR exome

AF:

0.247

Gnomad AMR exome

AF:

0.106

Gnomad ASJ exome

AF:

0.0407

Gnomad EAS exome

AF:

0.00192

Gnomad SAS exome

AF:

0.0208

Gnomad FIN exome

AF:

0.0516

Gnomad NFE exome

AF:

0.0264

Gnomad OTH exome

AF:

0.0368

GnomAD4 exome

AF:

0.0814

AC:

118855

AN:

1460428

Hom.:

7050

Cov.:

AF XY:

0.0791

AC XY:

57471

AN XY:

726336

show subpopulations

Gnomad4 AFR exome

AF:

0.374

Gnomad4 AMR exome

AF:

0.206

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:

0.0913

GnomAD4 genome

AF:

0.165

AC:

25032

AN:

152106

Hom.:

3331

Cov.:

AF XY:

0.164

AC XY:

12204

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.373

Gnomad4 AMR

AF:

0.162

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:

0.0211

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