rs7254232

Positions:

• chr19-47293543-A-G
• chr19-47293543-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000595501.5(C5AR1):​n.235+1370A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 151,976 control chromosomes in the GnomAD database, including 8,582 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 0.33 (8582 hom., cov: 31)
• Consequence: C5AR1 ENST00000595501.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647

Genes affected

C5AR1 (HGNC:1338): (complement C5a receptor 1) Enables G protein-coupled receptor activity and complement component C5a receptor activity. Involved in several processes, including complement component C5a signaling pathway; mRNA transcription by RNA polymerase II; and positive regulation of ERK1 and ERK2 cascade. Located in apical part of cell and basolateral plasma membrane. Biomarker of Alzheimer's disease; asthma; chronic obstructive pulmonary disease; rhinitis; and severe acute respiratory syndrome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C5AR1	ENST00000595501.5	n.235+1370A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.329 AC: 50014 AN: 151860 Hom.: 8573 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.329 AC: 50040 AN: 151976 Hom.: 8582 Cov.: 31 AF XY: 0.335 AC XY: 24858 AN XY: 74280

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.335

Alfa AF: 0.310 Hom.: 3318

Bravo AF: 0.330

Asia WGS AF: 0.480 AC: 1668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.021
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7254232; hg19: chr19-47796800;