Menu
GeneBe

1-161626220-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_001244753.2(FCGR3B):c.502G>A(p.Gly168Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000115 in 1,608,584 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00059 ( 6 hom., cov: 28)
Exomes 𝑓: 0.000067 ( 4 hom. )

Consequence

FCGR3B
NM_001244753.2 missense

Scores

2
10

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.49
Variant links:
Genes affected
FCGR3B (HGNC:3620): (Fc gamma receptor IIIb) The protein encoded by this gene is a low affinity receptor for the Fc region of gamma immunoglobulins (IgG). The encoded protein acts as a monomer and can bind either monomeric or aggregated IgG. This gene may function to capture immune complexes in the peripheral circulation. Several transcript variants encoding different isoforms have been found for this gene. A highly-similar gene encoding a related protein is also found on chromosome 1. [provided by RefSeq, Aug 2012]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (MetaRNN=0.057602435).
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 6 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FCGR3BNM_001244753.2 linkuse as main transcriptc.502G>A p.Gly168Ser missense_variant 4/5 ENST00000650385.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FCGR3BENST00000650385.1 linkuse as main transcriptc.502G>A p.Gly168Ser missense_variant 4/5 NM_001244753.2 P2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000580
AC:
87
AN:
150128
Hom.:
6
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.00194
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000133
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000194
Gnomad SAS
AF:
0.000424
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000591
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000176
AC:
44
AN:
250412
Hom.:
0
AF XY:
0.000140
AC XY:
19
AN XY:
135334
show subpopulations
Gnomad AFR exome
AF:
0.00149
Gnomad AMR exome
AF:
0.000261
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000706
Gnomad OTH exome
AF:
0.000164
GnomAD4 exome
AF:
0.0000665
AC:
97
AN:
1458340
Hom.:
4
Cov.:
33
AF XY:
0.0000607
AC XY:
44
AN XY:
725414
show subpopulations
Gnomad4 AFR exome
AF:
0.00160
Gnomad4 AMR exome
AF:
0.000292
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000505
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000225
Gnomad4 OTH exome
AF:
0.0000664
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000586
AC:
88
AN:
150244
Hom.:
6
Cov.:
28
AF XY:
0.000695
AC XY:
51
AN XY:
73402
show subpopulations
Gnomad4 AFR
AF:
0.00196
Gnomad4 AMR
AF:
0.000133
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000195
Gnomad4 SAS
AF:
0.000425
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000591
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000384
Hom.:
3
Bravo
AF:
0.000676
ESP6500AA
AF:
0.00205
AC:
9
ESP6500EA
AF:
0.000233
AC:
2
ExAC
?
    Exome Aggregation Consortium database
AF:
0.000198
AC:
24

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsAug 10, 2021The c.502G>A (p.G168S) alteration is located in exon 5 (coding exon 4) of the FCGR3B gene. This alteration results from a G to A substitution at nucleotide position 502, causing the glycine (G) at amino acid position 168 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.50
BayesDel_addAF
Benign
-0.32
T
BayesDel_noAF
Benign
-0.25
Cadd
Uncertain
25
Dann
Uncertain
0.99
Eigen
Benign
-0.033
Eigen_PC
Benign
-0.18
FATHMM_MKL
Benign
0.49
N
M_CAP
Benign
0.020
T
MetaRNN
Benign
0.058
T;T;T;T;T
MetaSVM
Benign
-0.76
T
MutationTaster
Benign
1.0
D;D;D;D;D;N;N;N
PrimateAI
Benign
0.43
T
Vest4
0.74, 0.73, 0.68, 0.67
MVP
0.47
MPC
0.57
ClinPred
0.33
T
GERP RS
2.5
gMVP
0.75

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: rs188904436; hg19: chr1-161596010; COSMIC: COSV54208880; COSMIC: COSV54208880; API