rs11567805

Variant names:

• chr12-8059976-G-A
• rs11567805
• NM_004054.4:c.210C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-8059976-G-A
• chr12-8059976-G-C
• chr12-8059976-G-T

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_004054.4(C3AR1):​c.210C>T​(p.Leu70Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.012 in 1,614,098 control chromosomes in the GnomAD database, including 855 homozygotes. 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: 𝑓 0.029 (175 hom., cov: 32)
  • Exomes 𝑓: 0.010 (680 hom.)
• Consequence: C3AR1 NM_004054.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65
• Publications: 5 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: Benign. The variant received -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BP7: Synonymous conserved (PhyloP=1.65 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0891 is higher than 0.05.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C3AR1	NM_004054.4	MANE Select	c.210C>T	p.Leu70Leu	synonymous	Exon 2 of 2	NP_004045.1	A8K2H7
	C3AR1	NM_001326475.2		c.210C>T	p.Leu70Leu	synonymous	Exon 2 of 2	NP_001313404.1	A8K2H7
	C3AR1	NM_001326477.2		c.210C>T	p.Leu70Leu	synonymous	Exon 2 of 2	NP_001313406.1	Q16581

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C3AR1	ENST00000307637.5	TSL:1 MANE Select	c.210C>T	p.Leu70Leu	synonymous	Exon 2 of 2	ENSP00000302079.4	Q16581
	C3AR1	ENST00000904894.1		c.210C>T	p.Leu70Leu	synonymous	Exon 2 of 2	ENSP00000574953.1
	C3AR1	ENST00000904895.1		c.210C>T	p.Leu70Leu	synonymous	Exon 2 of 2	ENSP00000574954.1

Frequencies

GnomAD3 genomes AF: 0.0288 AC: 4379 AN: 152114 Hom.: 175 Cov.: 32

Gnomad AFR AF: 0.0783

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0175

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0603

Gnomad SAS AF: 0.0971

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000662

Gnomad OTH AF: 0.0205

GnomAD2 exomes AF: 0.0251 AC: 6316 AN: 251332 AF XY: 0.0261

Gnomad AFR exome AF: 0.0809

Gnomad AMR exome AF: 0.0227

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0635

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000739

Gnomad OTH exome AF: 0.0126

GnomAD4 exome AF: 0.0102 AC: 14957 AN: 1461866 Hom.: 680 Cov.: 33 AF XY: 0.0121 AC XY: 8781 AN XY: 727234

African (AFR) AF: 0.0797 AC: 2668 AN: 33478

American (AMR) AF: 0.0213 AC: 951 AN: 44710

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.0539 AC: 2139 AN: 39700

South Asian (SAS) AF: 0.0897 AC: 7736 AN: 86256

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53420

Middle Eastern (MID) AF: 0.00676 AC: 39 AN: 5768

European-Non Finnish (NFE) AF: 0.000390 AC: 434 AN: 1112004

Other (OTH) AF: 0.0164 AC: 990 AN: 60394

GnomAD4 genome AF: 0.0288 AC: 4381 AN: 152232 Hom.: 175 Cov.: 32 AF XY: 0.0296 AC XY: 2206 AN XY: 74450

African (AFR) AF: 0.0782 AC: 3246 AN: 41506

American (AMR) AF: 0.0175 AC: 268 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.0605 AC: 313 AN: 5176

South Asian (SAS) AF: 0.0963 AC: 464 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10622

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.000662 AC: 45 AN: 68018

Other (OTH) AF: 0.0203 AC: 43 AN: 2116

Alfa AF: 0.00971 Hom.: 67

Bravo AF: 0.0303

Asia WGS AF: 0.0680 AC: 238 AN: 3478

EpiCase AF: 0.000436

EpiControl AF: 0.000474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	9.4
DANN	Benign	0.78
PhyloP100		1.7
Mutation Taster		=83/17	polymorphism (auto)

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: rs11567805; hg19: chr12-8212572; COSMIC: COSV50821903; COSMIC: COSV50821903;