Variant chr1-161626196-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001244753.2(FCGR3B):c.526G>T(p.Val176Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00156 in 1,608,958 control chromosomes in the GnomAD database, including 74 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0016 ( 7 hom., cov: 28)

Exomes 𝑓: 0.0016 ( 67 hom. )

Consequence

FCGR3B
NM_001244753.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.384

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0057968795).

BP6

Variant 1-161626196-C-A is Benign according to our data. Variant chr1-161626196-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 3250532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-161626196-C-A is described in Lovd as [Likely_benign].

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCGR3B	NM_001244753.2 linkuse as main transcript	c.526G>T	p.Val176Phe	missense_variant	4/5	ENST00000650385.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCGR3B	ENST00000650385.1 linkuse as main transcript	c.526G>T	p.Val176Phe	missense_variant	4/5		NM_001244753.2	P2

Frequencies

GnomAD3 genomes

AF:

0.00156

AC:

235

AN:

150274

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00114

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00272

Gnomad ASJ

AF:

0.00289

Gnomad EAS

AF:

0.000581

Gnomad SAS

AF:

0.00612

Gnomad FIN

AF:

0.0000953

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00148

Gnomad OTH

AF:

0.00243

GnomAD3 exomes

AF:

0.00148

AC:

370

AN:

250400

Hom.:

AF XY:

0.00164

AC XY:

222

AN XY:

135362

show subpopulations

Gnomad AFR exome

AF:

0.000373

Gnomad AMR exome

AF:

0.00139

Gnomad ASJ exome

AF:

0.00169

Gnomad EAS exome

AF:

0.000273

Gnomad SAS exome

AF:

0.00426

Gnomad FIN exome

AF:

0.000139

Gnomad NFE exome

AF:

0.00132

Gnomad OTH exome

AF:

0.00180

GnomAD4 exome

AF:

0.00156

AC:

2273

AN:

1458570

Hom.:

Cov.:

AF XY:

0.00168

AC XY:

1217

AN XY:

725576

show subpopulations

Gnomad4 AFR exome

AF:

0.000693

Gnomad4 AMR exome

AF:

0.00184

Gnomad4 ASJ exome

AF:

0.00146

Gnomad4 EAS exome

AF:

0.000151

Gnomad4 SAS exome

AF:

0.00481

Gnomad4 FIN exome

AF:

0.000150

Gnomad4 NFE exome

AF:

0.00143

Gnomad4 OTH exome

AF:

0.00179

GnomAD4 genome

AF:

0.00156

AC:

234

AN:

150388

Hom.:

Cov.:

AF XY:

0.00163

AC XY:

120

AN XY:

73448

show subpopulations

Gnomad4 AFR

AF:

0.00114

Gnomad4 AMR

AF:

0.00272

Gnomad4 ASJ

AF:

0.00289

Gnomad4 EAS

AF:

0.000582

Gnomad4 SAS

AF:

0.00592

Gnomad4 FIN

AF:

0.0000953

Gnomad4 NFE

AF:

0.00148

Gnomad4 OTH

AF:

0.00241

Alfa

AF:

0.000883

Hom.:

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.000581

AC:

ExAC

AF:

0.00176

AC:

213

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jun 01, 2024

FCGR3B: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.21

BayesDel_addAF

Benign

-0.54

BayesDel_noAF

Benign

-0.55

CADD

Benign

1.4

DANN

Benign

0.68

DEOGEN2

Benign

0.031

.;.;T;.;.

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.8

FATHMM_MKL

Benign

0.0083

LIST_S2

Benign

0.20

.;.;T;T;T

M_CAP

Benign

0.0027

MetaRNN

Benign

0.0058

T;T;T;T;T

MetaSVM

Benign

-0.97

MutationTaster

Benign

1.0

N;N;N;N;N;N;N;N

PrimateAI

Benign

0.34

PROVEAN

Benign

-2.1

.;N;.;N;N

REVEL

Benign

0.11

Sift

Benign

0.037

.;D;.;D;T

Sift4G

Uncertain

0.028

.;D;D;D;D

Vest4

0.40, 0.42, 0.41, 0.39

MVP

0.055

MPC

0.27

ClinPred

0.0057

GERP RS

-2.1

gMVP

0.37

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over