rs7254232

Variant names:

• chr19-47293543-A-G
• rs7254232
• ENST00000595501.5:n.235+1370A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000595501.5(C5AR1):​n.235+1370A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C5AR1	ENST00000595501.5	n.235+1370A>G		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.362 AC: 14984 AN: 41374

American (AMR) AF: 0.351 AC: 5354 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1380 AN: 3472

East Asian (EAS) AF: 0.492 AC: 2548 AN: 5176

South Asian (SAS) AF: 0.511 AC: 2466 AN: 4824

European-Finnish (FIN) AF: 0.304 AC: 3220 AN: 10582

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19016 AN: 67970

Other (OTH) AF: 0.335 AC: 708 AN: 2116

Alfa AF: 0.308 Hom.: 3644

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
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs7254232; hg19: chr19-47796800;