rs550458778

Variant names:

• chr6-116792598-A-AG
• rs550458778
• NM_148963.4:c.2324_2325insC

Your query was ambiguous. Multiple possible variants found:

• chr6-116792598-A-AG
• chr6-116792598-A-AGG
• chr6-116792598-A-AGGT
• chr6-116792598-A-AGGTAAT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_148963.4(GPRC6A):​c.2324_2325insC​(p.Glu776fs) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: GPRC6A NM_148963.4 frameshift
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.75

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPRC6A	NM_148963.4	c.2324_2325insC	p.Glu776fs	frameshift_variant	Exon 6 of 6	ENST00000310357.8	NP_683766.2
GPRC6A	NM_001286355.1	c.2111_2112insC	p.Glu705fs	frameshift_variant	Exon 5 of 5		NP_001273284.1
GPRC6A	NM_001286354.1	c.1799_1800insC	p.Glu601fs	frameshift_variant	Exon 6 of 6		NP_001273283.1
GPRC6A	XM_017010475.2	c.2183_2184insC	p.Glu729fs	frameshift_variant	Exon 7 of 7		XP_016865964.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPRC6A	ENST00000310357.8	c.2324_2325insC	p.Glu776fs	frameshift_variant	Exon 6 of 6	1	NM_148963.4	ENSP00000309493.4
GPRC6A	ENST00000368549.7	c.2111_2112insC	p.Glu705fs	frameshift_variant	Exon 5 of 5	1		ENSP00000357537.3
GPRC6A	ENST00000530250.1	c.1799_1800insC	p.Glu601fs	frameshift_variant	Exon 6 of 6	1		ENSP00000433465.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 37

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs550458778; hg19: chr6-117113761;