Variant 1-161629864-G-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001244753.2(FCGR3B):c.233C>A(p.Ala78Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0305 in 1,486,942 control chromosomes in the GnomAD database, including 4,465 homozygotes. 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 same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.075 ( 1102 hom., cov: 10)

Exomes 𝑓: 0.028 ( 3363 hom. )

Consequence

FCGR3B
NM_001244753.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.01

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:

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=0.0067406297).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCGR3B	NM_001244753.2 linkuse as main transcript	c.233C>A	p.Ala78Asp	missense_variant	3/5	ENST00000650385.1	NP_001231682.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCGR3B	ENST00000650385.1 linkuse as main transcript	c.233C>A	p.Ala78Asp	missense_variant	3/5		NM_001244753.2	ENSP00000497461	P2

Frequencies

GnomAD3 genomes

AF:

0.0748

AC:

6124

AN:

81818

Hom.:

1102

Cov.:

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.0490

Gnomad AMR

AF:

0.0386

Gnomad ASJ

AF:

0.0218

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.0344

Gnomad MID

AF:

0.0482

Gnomad NFE

AF:

0.0292

Gnomad OTH

AF:

0.0589

GnomAD3 exomes

AF:

0.0378

AC:

9301

AN:

245862

Hom.:

971

AF XY:

0.0374

AC XY:

4990

AN XY:

133314

show subpopulations

Gnomad AFR exome

AF:

0.195

Gnomad AMR exome

AF:

0.0194

Gnomad ASJ exome

AF:

0.0238

Gnomad EAS exome

AF:

0.000170

Gnomad SAS exome

AF:

0.0756

Gnomad FIN exome

AF:

0.0261

Gnomad NFE exome

AF:

0.0216

Gnomad OTH exome

AF:

0.0313

GnomAD4 exome

AF:

0.0279

AC:

39227

AN:

1405084

Hom.:

3363

Cov.:

AF XY:

0.0294

AC XY:

20540

AN XY:

697870

show subpopulations

Gnomad4 AFR exome

AF:

0.207

Gnomad4 AMR exome

AF:

0.0214

Gnomad4 ASJ exome

AF:

0.0241

Gnomad4 EAS exome

AF:

0.0000317

Gnomad4 SAS exome

AF:

0.0847

Gnomad4 FIN exome

AF:

0.0258

Gnomad4 NFE exome

AF:

0.0197

Gnomad4 OTH exome

AF:

0.0339

GnomAD4 genome

AF:

0.0749

AC:

6131

AN:

81858

Hom.:

1102

Cov.:

AF XY:

0.0762

AC XY:

2931

AN XY:

38460

show subpopulations

Gnomad4 AFR

AF:

0.228

Gnomad4 AMR

AF:

0.0386

Gnomad4 ASJ

AF:

0.0218

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.120

Gnomad4 FIN

AF:

0.0344

Gnomad4 NFE

AF:

0.0291

Gnomad4 OTH

AF:

0.0582

Alfa

AF:

0.0147

Hom.:

ESP6500AA

AF:

0.194

AC:

839

ESP6500EA

AF:

0.0199

AC:

171

ExAC

AF:

0.0418

AC:

5053

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.62

CADD

Benign

0.019

DANN

Benign

0.60

DEOGEN2

Benign

0.020

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

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.0047

LIST_S2

Benign

0.21

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

MetaRNN

Benign

0.0067

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

MetaSVM

Benign

-0.94

MutationTaster

Benign

1.0

P;P;P;P;P;P;P;P

PrimateAI

Benign

0.31

PROVEAN

Benign

-0.84

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

REVEL

Benign

0.023

Sift

Benign

0.34

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

Sift4G

Benign

0.48

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

Vest4

0.11, 0.14, 0.12, 0.087, 0.10

MPC

2.3

ClinPred

0.00048

GERP RS

-4.0

gMVP

0.20

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