rs4806608

Variant names:

• chr19-54884171-A-G
• rs4806608
• NM_002000.4:c.71-1064A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002000.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCAR	NM_002000.4	MANE Select	c.71-1064A>G		intron	N/A	NP_001991.1
	FCAR	NM_133272.4		c.35-1064A>G		intron	N/A	NP_579806.1
	FCAR	NM_133269.4		c.71-1064A>G		intron	N/A	NP_579803.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCAR	ENST00000355524.8	TSL:1 MANE Select	c.71-1064A>G		intron	N/A	ENSP00000347714.3
	FCAR	ENST00000359272.8	TSL:1	c.35-1064A>G		intron	N/A	ENSP00000352218.4
	FCAR	ENST00000391725.7	TSL:1	c.71-1064A>G		intron	N/A	ENSP00000375605.3

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

African (AFR) AF: 0.153 AC: 6353 AN: 41520

American (AMR) AF: 0.142 AC: 2166 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1147 AN: 3470

East Asian (EAS) AF: 0.137 AC: 706 AN: 5158

South Asian (SAS) AF: 0.131 AC: 633 AN: 4820

European-Finnish (FIN) AF: 0.172 AC: 1820 AN: 10592

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13722 AN: 67970

Other (OTH) AF: 0.191 AC: 404 AN: 2110

Alfa AF: 0.202 Hom.: 3402

Bravo AF: 0.177

Asia WGS AF: 0.133 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.9
DANN	Benign	0.66
PhyloP100		-1.8
Mutation Taster		=100/0	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: rs4806608; hg19: chr19-55395582;