Variant 1-161629989-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001244753.2(FCGR3B):c.108C>G(p.Ser36Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/18 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 the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.00071 ( 1 hom., cov: 17)

Exomes 𝑓: 0.0039 ( 2339 hom. )

Failed GnomAD Quality Control

Consequence

FCGR3B
NM_001244753.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01

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]

FCGR3B links:

ENSG00000289768 (HGNC:):

ENSG00000289768 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0085681975).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCGR3B	NM_001244753.2 link	c.108C>G	p.Ser36Arg	missense_variant	Exon 3 of 5	ENST00000650385.1	NP_001231682.2	O75015

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCGR3B	ENST00000650385.1 link	c.108C>G	p.Ser36Arg	missense_variant	Exon 3 of 5		NM_001244753.2	ENSP00000497461.1		A0A3B3ISU3
ENSG00000289768	ENST00000699402.1 link	c.40+1066C>G		intron_variant	Intron 1 of 3			ENSP00000514363.1		A0A8V8TN80

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

107672

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000518

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000943

Gnomad ASJ

AF:

0.000345

Gnomad EAS

AF:

0.00253

Gnomad SAS

AF:

0.00142

Gnomad FIN

AF:

0.000128

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000775

Gnomad OTH

AF:

0.000686

GnomAD3 exomes

AF:

0.0115

AC:

2393

AN:

208406

Hom.:

1169

AF XY:

0.0114

AC XY:

1285

AN XY:

113140

show subpopulations

Gnomad AFR exome

AF:

0.0137

Gnomad AMR exome

AF:

0.0156

Gnomad ASJ exome

AF:

0.00311

Gnomad EAS exome

AF:

0.0566

Gnomad SAS exome

AF:

0.0149

Gnomad FIN exome

AF:

0.00140

Gnomad NFE exome

AF:

0.00672

Gnomad OTH exome

AF:

0.0119

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00388

AC:

4861

AN:

1252378

Hom.:

2339

Cov.:

AF XY:

0.00434

AC XY:

2701

AN XY:

622174

show subpopulations

Gnomad4 AFR exome

AF:

0.00552

Gnomad4 AMR exome

AF:

0.0155

Gnomad4 ASJ exome

AF:

0.00206

Gnomad4 EAS exome

AF:

0.0271

Gnomad4 SAS exome

AF:

0.0152

Gnomad4 FIN exome

AF:

0.00220

Gnomad4 NFE exome

AF:

0.00216

Gnomad4 OTH exome

AF:

0.00431

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000715

AC:

AN:

107726

Hom.:

Cov.:

AF XY:

0.000712

AC XY:

AN XY:

51976

show subpopulations

Gnomad4 AFR

AF:

0.000516

Gnomad4 AMR

AF:

0.000943

Gnomad4 ASJ

AF:

0.000345

Gnomad4 EAS

AF:

0.00253

Gnomad4 SAS

AF:

0.00143

Gnomad4 FIN

AF:

0.000128

Gnomad4 NFE

AF:

0.000775

Gnomad4 OTH

AF:

0.000681

Alfa

AF:

0.0145

Hom.:

ExAC

AF:

0.000386

AC:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.045

BayesDel_addAF

Benign

-0.32

BayesDel_noAF

Benign

-0.69

CADD

Benign

0.23

DANN

Benign

0.43

DEOGEN2

Benign

0.0034

.;.;T;.;.;.;T

Eigen

Benign

-1.9

Eigen_PC

Benign

-2.0

FATHMM_MKL

Benign

0.00075

LIST_S2

Benign

0.076

.;.;T;T;T;T;T

MetaRNN

Benign

0.0086

T;T;T;T;T;T;T

MetaSVM

Benign

-0.98

PrimateAI

Benign

0.35

PROVEAN

Benign

2.2

.;N;.;.;N;N;N

REVEL

Benign

0.016

Sift

Benign

1.0

.;T;.;.;T;T;T

Sift4G

Benign

0.52

.;T;T;T;T;T;.

Vest4

0.17, 0.20, 0.20, 0.18, 0.19

MutPred

0.40

Loss of ubiquitination at K40 (P = 0.0768);Loss of ubiquitination at K40 (P = 0.0768);.;.;Loss of ubiquitination at K40 (P = 0.0768);.;.;

MPC

0.010

ClinPred

0.00066

GERP RS

-5.1

gMVP

0.27

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over