Variant 12-8059976-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.65

Variant links:

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]

C3AR1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C3AR1	NM_004054.4 linkuse as main transcript	c.210C>T	p.Leu70Leu	synonymous_variant	2/2	ENST00000307637.5	NP_004045.1	Q16581A8K2H7
C3AR1	NM_001326475.2 linkuse as main transcript	c.210C>T	p.Leu70Leu	synonymous_variant	2/2		NP_001313404.1	Q16581A8K2H7
C3AR1	NM_001326477.2 linkuse as main transcript	c.210C>T	p.Leu70Leu	synonymous_variant	2/2		NP_001313406.1	Q16581A8K2H7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C3AR1	ENST00000307637.5 linkuse as main transcript	c.210C>T	p.Leu70Leu	synonymous_variant	2/2	1	NM_004054.4	ENSP00000302079.4		Q16581
C3AR1	ENST00000546241.1 linkuse as main transcript	c.210C>T	p.Leu70Leu	synonymous_variant	2/2	4		ENSP00000444500.1		F5GZE6

Frequencies

GnomAD3 genomes

AF:

0.0288

AC:

4379

AN:

152114

Hom.:

175

Cov.:

show subpopulations

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

GnomAD3 exomes

AF:

0.0251

AC:

6316

AN:

251332

Hom.:

279

AF XY:

0.0261

AC XY:

3547

AN XY:

135844

show subpopulations

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 SAS exome

AF:

0.0944

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.:

AF XY:

0.0121

AC XY:

8781

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.0797

Gnomad4 AMR exome

AF:

0.0213

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0539

Gnomad4 SAS exome

AF:

0.0897

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000390

Gnomad4 OTH exome

AF:

0.0164

GnomAD4 genome

AF:

0.0288

AC:

4381

AN:

152232

Hom.:

175

Cov.:

AF XY:

0.0296

AC XY:

2206

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.0782

Gnomad4 AMR

AF:

0.0175

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0605

Gnomad4 SAS

AF:

0.0963

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000662

Gnomad4 OTH

AF:

0.0203

Alfa

AF:

0.00753

Hom.:

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

9.4

DANN

Benign

0.78

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over