NM_001002901.4:c.584G>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001002901.4(FCRLB):​c.584G>C​(p.Arg195Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000694 in 1,440,944 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. R195L) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 6.9e-7 ( 0 hom. )

Consequence

FCRLB
NM_001002901.4 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.146
Variant links:
Genes affected
FCRLB (HGNC:26431): (Fc receptor like B) FCRL2 belongs to the Fc receptor family. Fc receptors are involved in phagocytosis, antibody-dependent cell cytotoxicity, immediate hypersensitivity, and transcytosis of immunoglobulins via their ability to bind immunoglobulin (Ig) constant regions (Chikaev et al., 2005 [PubMed 15676285]).[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.027767926).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FCRLBNM_001002901.4 linkc.584G>C p.Arg195Pro missense_variant Exon 7 of 8 ENST00000367948.7 NP_001002901.1 Q6BAA4-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FCRLBENST00000367948.7 linkc.584G>C p.Arg195Pro missense_variant Exon 7 of 8 1 NM_001002901.4 ENSP00000356925.2 Q6BAA4-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.94e-7
AC:
1
AN:
1440944
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
716350
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000167
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.046
BayesDel_addAF
Benign
-0.34
T
BayesDel_noAF
Benign
-0.72
CADD
Benign
7.1
DANN
Benign
0.86
DEOGEN2
Benign
0.019
T
Eigen
Benign
-1.4
Eigen_PC
Benign
-1.2
FATHMM_MKL
Benign
0.020
N
LIST_S2
Benign
0.26
T
M_CAP
Benign
0.012
T
MetaRNN
Benign
0.028
T
MetaSVM
Benign
-0.96
T
MutationAssessor
Benign
-1.6
N
PrimateAI
Benign
0.47
T
PROVEAN
Benign
3.5
N
REVEL
Benign
0.062
Sift
Benign
1.0
T
Sift4G
Benign
0.26
T
Polyphen
0.0
B
Vest4
0.10
MutPred
0.53
Loss of MoRF binding (P = 0.0031);
MVP
0.12
MPC
1.0
ClinPred
0.065
T
GERP RS
-1.3
Varity_R
0.13
gMVP
0.53

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs1285386417; hg19: chr1-161696502; API