rs4806608

chr19-54884171-A-G

Variant summary

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

The NM_002000.4(FCAR):c.71-1064A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,124 control chromosomes in the GnomAD database, including 2,557 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 0.18 (2557 hom., cov: 32)
• Consequence: FCAR NM_002000.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

Genes affected

FCAR (HGNC:3608): (Fc alpha receptor) This gene is a member of the immunoglobulin gene superfamily and encodes a receptor for the Fc region of IgA. The receptor is a transmembrane glycoprotein present on the surface of myeloid lineage cells such as neutrophils, monocytes, macrophages, and eosinophils, where it mediates immunologic responses to pathogens. It interacts with IgA-opsonized targets and triggers several immunologic defense processes, including phagocytosis, antibody-dependent cell-mediated cytotoxicity, and stimulation of the release of inflammatory mediators. Multiple alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCAR	NM_002000.4	c.71-1064A>G		intron_variant		ENST00000355524.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCAR	ENST00000355524.8	c.71-1064A>G		intron_variant		1	NM_002000.4	P2

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27203 AN: 152006 Hom.: 2558 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.179 AC: 27220 AN: 152124 Hom.: 2557 Cov.: 32 AF XY: 0.175 AC XY: 13008 AN XY: 74354

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.191

Alfa AF: 0.209 Hom.: 2594

Bravo AF: 0.177

Asia WGS AF: 0.133 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	4.9
Dann	Benign	0.66

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

Other links and lift over

dbSNP: rs4806608; hg19: chr19-55395582;