19-47340992-CGC-TGT

Variant names:

• chr19-47340992-CGC-TGT
• NM_001271749.2:c.193_195delCGCinsTGT
• C5AR2 p.Arg65Cys

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001271749.2(C5AR2):​c.193_195delCGCinsTGT​(p.Arg65Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: C5AR2 NM_001271749.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486
• Publications: 0 publications found

Genes affected

C5AR2 (HGNC:4527): (complement C5a receptor 2) This gene encodes a G-protein coupled receptor 1 family member involved in the complement system of the innate immune response. Unlike classical G-protein coupled receptors, the encoded protein does not associate with intracellular G-proteins. It may instead modulate signal transduction through the beta-arrestin pathway, and may alternatively act as a decoy receptor. This gene may be involved in coronary artery disease and in the pathogenesis of sepsis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001271749.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C5AR2	NM_001271749.2	MANE Select	c.193_195delCGCinsTGT	p.Arg65Cys	missense	N/A	NP_001258678.1	Q9P296
	C5AR2	NM_001271750.2		c.193_195delCGCinsTGT	p.Arg65Cys	missense	N/A	NP_001258679.1	Q9P296
	C5AR2	NM_018485.3		c.193_195delCGCinsTGT	p.Arg65Cys	missense	N/A	NP_060955.1	Q9P296

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C5AR2	ENST00000595464.3	TSL:1 MANE Select	c.193_195delCGCinsTGT	p.Arg65Cys	missense	N/A	ENSP00000472620.1	Q9P296
	C5AR2	ENST00000600626.1	TSL:1	c.193_195delCGCinsTGT	p.Arg65Cys	missense	N/A	ENSP00000471184.1	Q9P296
	C5AR2	ENST00000874258.1		c.193_195delCGCinsTGT	p.Arg65Cys	missense	N/A	ENSP00000544317.1

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr19-47844249;