rs2304225

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002000.4(FCAR):​c.34+183C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0521 in 152,192 control chromosomes in the GnomAD database, including 319 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 0.052 ( 319 hom., cov: 32)

Consequence

FCAR
NM_002000.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.360
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FCARNM_002000.4 linkuse as main transcriptc.34+183C>G intron_variant ENST00000355524.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FCARENST00000355524.8 linkuse as main transcriptc.34+183C>G intron_variant 1 NM_002000.4 P2P24071-1

Frequencies

GnomAD3 genomes
AF:
0.0521
AC:
7919
AN:
152074
Hom.:
319
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0121
Gnomad AMI
AF:
0.0976
Gnomad AMR
AF:
0.0790
Gnomad ASJ
AF:
0.0441
Gnomad EAS
AF:
0.158
Gnomad SAS
AF:
0.0469
Gnomad FIN
AF:
0.0398
Gnomad MID
AF:
0.0285
Gnomad NFE
AF:
0.0644
Gnomad OTH
AF:
0.0559
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0521
AC:
7922
AN:
152192
Hom.:
319
Cov.:
32
AF XY:
0.0518
AC XY:
3853
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.0120
Gnomad4 AMR
AF:
0.0790
Gnomad4 ASJ
AF:
0.0441
Gnomad4 EAS
AF:
0.158
Gnomad4 SAS
AF:
0.0471
Gnomad4 FIN
AF:
0.0398
Gnomad4 NFE
AF:
0.0644
Gnomad4 OTH
AF:
0.0577
Alfa
AF:
0.0372
Hom.:
34
Bravo
AF:
0.0526
Asia WGS
AF:
0.113
AC:
394
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.92
DANN
Benign
0.34

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.

Other links and lift over

dbSNP: rs2304225; hg19: chr19-55385962; API