Variant chr1-161673191-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_001394477.1(FCGR2B):c.608C>T(p.Thr203Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000873 in 150,048 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. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00087 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0028 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

FCGR2B
NM_001394477.1 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.77

Variant links:

Genes affected

FCGR2B (HGNC:3618): (Fc gamma receptor IIb) The protein encoded by this gene is a low affinity receptor for the Fc region of immunoglobulin gamma complexes. The encoded protein is involved in the phagocytosis of immune complexes and in the regulation of antibody production by B-cells. Variations in this gene may increase susceptibilty to systemic lupus erythematosus (SLE). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]

FCGR2B links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0041023493).

BP6

Variant 1-161673191-C-T is Benign according to our data. Variant chr1-161673191-C-T is described in ClinVar as [Benign]. Clinvar id is 2639516.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-161673191-C-T is described in Lovd as [Likely_benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCGR2B	NM_001394477.1 linkuse as main transcript	c.608C>T	p.Thr203Met	missense_variant	4/8	ENST00000358671.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCGR2B	ENST00000358671.10 linkuse as main transcript	c.608C>T	p.Thr203Met	missense_variant	4/8	1	NM_001394477.1	P4	P31994-1
	ENST00000453111.1 linkuse as main transcript	n.198-908G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.000874

AC:

131

AN:

149930

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000197

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000933

Gnomad ASJ

AF:

0.000290

Gnomad EAS

AF:

0.00290

Gnomad SAS

AF:

0.000849

Gnomad FIN

AF:

0.000961

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00116

Gnomad OTH

AF:

0.000486

GnomAD3 exomes

AF:

0.00237

AC:

585

AN:

246460

Hom.:

AF XY:

0.00254

AC XY:

338

AN XY:

133278

show subpopulations

Gnomad AFR exome

AF:

0.000843

Gnomad AMR exome

AF:

0.000907

Gnomad ASJ exome

AF:

0.00141

Gnomad EAS exome

AF:

0.00208

Gnomad SAS exome

AF:

0.00151

Gnomad FIN exome

AF:

0.00432

Gnomad NFE exome

AF:

0.00304

Gnomad OTH exome

AF:

0.00217

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00281

AC:

4068

AN:

1449216

Hom.:

Cov.:

AF XY:

0.00273

AC XY:

1968

AN XY:

720618

show subpopulations

Gnomad4 AFR exome

AF:

0.000391

Gnomad4 AMR exome

AF:

0.000564

Gnomad4 ASJ exome

AF:

0.00100

Gnomad4 EAS exome

AF:

0.00237

Gnomad4 SAS exome

AF:

0.000819

Gnomad4 FIN exome

AF:

0.00229

Gnomad4 NFE exome

AF:

0.00327

Gnomad4 OTH exome

AF:

0.00187

GnomAD4 genome

AF:

0.000873

AC:

131

AN:

150048

Hom.:

Cov.:

AF XY:

0.000818

AC XY:

AN XY:

73334

show subpopulations

Gnomad4 AFR

AF:

0.000196

Gnomad4 AMR

AF:

0.000931

Gnomad4 ASJ

AF:

0.000290

Gnomad4 EAS

AF:

0.00291

Gnomad4 SAS

AF:

0.000850

Gnomad4 FIN

AF:

0.000961

Gnomad4 NFE

AF:

0.00116

Gnomad4 OTH

AF:

0.000481

Alfa

AF:

0.00186

Hom.:

ESP6500AA

AF:

0.000912

AC:

ESP6500EA

AF:

0.00431

AC:

ExAC

AF:

0.00468

AC:

568

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

May 01, 2022

FCGR2B: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.32

BayesDel_noAF

Benign

-0.70

CADD

Benign

0.0010

DANN

Benign

0.40

DEOGEN2

Benign

0.038

.;.;T

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.0030

LIST_S2

Benign

0.72

T;T;T

M_CAP

Benign

0.016

MetaRNN

Benign

0.0041

T;T;T

MetaSVM

Benign

-0.89

MutationAssessor

Benign

-0.18

N;.;N

MutationTaster

Benign

1.0

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

PrimateAI

Benign

0.26

PROVEAN

Benign

-1.1

N;N;N

REVEL

Benign

0.046

Sift

Benign

0.36

T;T;T

Sift4G

Benign

0.58

T;T;T

Polyphen

0.38

B;B;P

Vest4

0.11

MVP

0.040

MPC

0.79

ClinPred

0.0079

GERP RS

-10

Varity_R

0.085

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over