rs2230318

Variant names:

• chr12-8058660-C-A
• rs2230318
• NM_004054.4:c.*77G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-8058660-C-A
• chr12-8058660-C-G
• chr12-8058660-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_004054.4(C3AR1):​c.*77G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: C3AR1 NM_004054.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.702
• Publications: 0 publications found

Genes affected

C3AR1 (HGNC:1319): (complement C3a receptor 1) C3a is an anaphylatoxin released during activation of the complement system. The protein encoded by this gene is an orphan G protein-coupled receptor for C3a. Binding of C3a by the encoded receptor activates chemotaxis, granule enzyme release, superoxide anion production, and bacterial opsonization. [provided by RefSeq, May 2016]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004054.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C3AR1	NM_004054.4	MANE Select	c.*77G>T		3_prime_UTR	Exon 2 of 2	NP_004045.1
	C3AR1	NM_001326475.2		c.*77G>T		3_prime_UTR	Exon 2 of 2	NP_001313404.1
	C3AR1	NM_001326477.2		c.*77G>T		3_prime_UTR	Exon 2 of 2	NP_001313406.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C3AR1	ENST00000307637.5	TSL:1 MANE Select	c.*77G>T		3_prime_UTR	Exon 2 of 2	ENSP00000302079.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1321396 Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0 AN XY: 652050

African (AFR) AF: 0.00 AC: 0 AN: 29478

American (AMR) AF: 0.00 AC: 0 AN: 32034

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20292

East Asian (EAS) AF: 0.00 AC: 0 AN: 38762

South Asian (SAS) AF: 0.00 AC: 0 AN: 70162

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 49824

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3622

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1022388

Other (OTH) AF: 0.00 AC: 0 AN: 54834

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.30
DANN	Benign	0.78
PhyloP100		-0.70

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

Other links and lift over

dbSNP: rs2230318; hg19: chr12-8211256;