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GeneBe

rs11666735

Variant summary

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

The NM_002000.4(FCAR):c.337G>A(p.Asp113Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0737 in 1,610,560 control chromosomes in the GnomAD database, including 4,670 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.066 ( 364 hom., cov: 32)
Exomes 𝑓: 0.075 ( 4306 hom. )

Consequence

FCAR
NM_002000.4 missense

Scores

1
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0290
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 (MetaRNN=0.0031760335).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0776 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FCARNM_002000.4 linkuse as main transcriptc.337G>A p.Asp113Asn missense_variant 3/5 ENST00000355524.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FCARENST00000355524.8 linkuse as main transcriptc.337G>A p.Asp113Asn missense_variant 3/51 NM_002000.4 P2P24071-1

Frequencies

GnomAD3 genomes
AF:
0.0655
AC:
9971
AN:
152150
Hom.:
363
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0466
Gnomad AMI
AF:
0.0340
Gnomad AMR
AF:
0.0545
Gnomad ASJ
AF:
0.128
Gnomad EAS
AF:
0.0402
Gnomad SAS
AF:
0.0698
Gnomad FIN
AF:
0.0588
Gnomad MID
AF:
0.0665
Gnomad NFE
AF:
0.0794
Gnomad OTH
AF:
0.0659
GnomAD3 exomes
AF:
0.0689
AC:
17257
AN:
250482
Hom.:
646
AF XY:
0.0704
AC XY:
9534
AN XY:
135488
show subpopulations
Gnomad AFR exome
AF:
0.0468
Gnomad AMR exome
AF:
0.0485
Gnomad ASJ exome
AF:
0.125
Gnomad EAS exome
AF:
0.0371
Gnomad SAS exome
AF:
0.0715
Gnomad FIN exome
AF:
0.0605
Gnomad NFE exome
AF:
0.0793
Gnomad OTH exome
AF:
0.0712
GnomAD4 exome
AF:
0.0745
AC:
108666
AN:
1458292
Hom.:
4306
Cov.:
32
AF XY:
0.0749
AC XY:
54332
AN XY:
725548
show subpopulations
Gnomad4 AFR exome
AF:
0.0460
Gnomad4 AMR exome
AF:
0.0485
Gnomad4 ASJ exome
AF:
0.122
Gnomad4 EAS exome
AF:
0.0341
Gnomad4 SAS exome
AF:
0.0707
Gnomad4 FIN exome
AF:
0.0647
Gnomad4 NFE exome
AF:
0.0775
Gnomad4 OTH exome
AF:
0.0765
GnomAD4 genome
AF:
0.0655
AC:
9976
AN:
152268
Hom.:
364
Cov.:
32
AF XY:
0.0649
AC XY:
4835
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.0466
Gnomad4 AMR
AF:
0.0544
Gnomad4 ASJ
AF:
0.128
Gnomad4 EAS
AF:
0.0403
Gnomad4 SAS
AF:
0.0705
Gnomad4 FIN
AF:
0.0588
Gnomad4 NFE
AF:
0.0794
Gnomad4 OTH
AF:
0.0652
Alfa
AF:
0.0784
Hom.:
934
Bravo
AF:
0.0642
TwinsUK
AF:
0.0825
AC:
306
ALSPAC
AF:
0.0669
AC:
258
ESP6500AA
AF:
0.0438
AC:
193
ESP6500EA
AF:
0.0824
AC:
709
ExAC
AF:
0.0691
AC:
8395
Asia WGS
AF:
0.0490
AC:
169
AN:
3478
EpiCase
AF:
0.0832
EpiControl
AF:
0.0826

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.095
BayesDel_addAF
Benign
-0.77
T
BayesDel_noAF
Benign
-0.81
Cadd
Benign
2.8
Dann
Benign
0.89
Eigen
Benign
-1.1
Eigen_PC
Benign
-1.2
FATHMM_MKL
Benign
0.018
N
MetaRNN
Benign
0.0032
T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.96
T
MutationTaster
Benign
1.0
N;N;N;N;N;N;N;N;N
PrimateAI
Benign
0.31
T
PROVEAN
Uncertain
-2.4
N;.;N;D;D;N;N;D
REVEL
Benign
0.020
Sift
Benign
0.60
T;.;T;T;T;T;T;T
Sift4G
Benign
0.32
T;T;T;T;T;T;T;T
Polyphen
0.0080, 0.12, 0.030
.;B;B;.;B;.;.;.
Vest4
0.15
MPC
0.056
ClinPred
0.0059
T
GERP RS
-0.13
Varity_R
0.25
gMVP
0.14

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs11666735; hg19: chr19-55396913; COSMIC: COSV62028915; API