Variant chr1-161674008-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001394477.1(FCGR2B):c.695T>C(p.Ile232Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as protective,risk factor (no stars).

Frequency

Genomes: 𝑓 0.19 ( 1242 hom., cov: 10)

Exomes 𝑓: 0.14 ( 3989 hom. )

Consequence

FCGR2B
NM_001394477.1 missense

Scores

Clinical Significance

protective; risk factor no assertion criteria provided B:1O:1

Conservation

PhyloP100: 0.740

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005741954).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCGR2B	NM_001394477.1 linkuse as main transcript	c.695T>C	p.Ile232Thr	missense_variant	5/8	ENST00000358671.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCGR2B	ENST00000358671.10 linkuse as main transcript	c.695T>C	p.Ile232Thr	missense_variant	5/8	1	NM_001394477.1	P4	P31994-1
	ENST00000453111.1 linkuse as main transcript	n.197+620A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.189

AC:

14950

AN:

78916

Hom.:

1237

Cov.:

show subpopulations

Gnomad AFR

AF:

0.276

Gnomad AMI

AF:

0.0651

Gnomad AMR

AF:

0.150

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.270

Gnomad SAS

AF:

0.164

Gnomad FIN

AF:

0.252

Gnomad MID

AF:

0.118

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.183

GnomAD3 exomes

AF:

0.161

AC:

11190

AN:

69660

Hom.:

977

AF XY:

0.159

AC XY:

5433

AN XY:

34256

show subpopulations

Gnomad AFR exome

AF:

0.254

Gnomad AMR exome

AF:

0.0993

Gnomad ASJ exome

AF:

0.123

Gnomad EAS exome

AF:

0.240

Gnomad SAS exome

AF:

0.141

Gnomad FIN exome

AF:

0.248

Gnomad NFE exome

AF:

0.122

Gnomad OTH exome

AF:

0.142

GnomAD4 exome

AF:

0.141

AC:

62003

AN:

438644

Hom.:

3989

Cov.:

AF XY:

0.141

AC XY:

32409

AN XY:

230286

show subpopulations

Gnomad4 AFR exome

AF:

0.248

Gnomad4 AMR exome

AF:

0.101

Gnomad4 ASJ exome

AF:

0.128

Gnomad4 EAS exome

AF:

0.237

Gnomad4 SAS exome

AF:

0.132

Gnomad4 FIN exome

AF:

0.205

Gnomad4 NFE exome

AF:

0.121

Gnomad4 OTH exome

AF:

0.146

GnomAD4 genome

AF:

0.190

AC:

14975

AN:

78964

Hom.:

1242

Cov.:

AF XY:

0.194

AC XY:

6879

AN XY:

35370

show subpopulations

Gnomad4 AFR

AF:

0.276

Gnomad4 AMR

AF:

0.150

Gnomad4 ASJ

AF:

0.134

Gnomad4 EAS

AF:

0.271

Gnomad4 SAS

AF:

0.164

Gnomad4 FIN

AF:

0.252

Gnomad4 NFE

AF:

0.135

Gnomad4 OTH

AF:

0.182

Alfa

AF:

0.150

Hom.:

217

ExAC

AF:

0.107

AC:

6193

ClinVar

Significance: protective; risk factor

Submissions summary: Benign:1Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Malaria, resistance to

Benign:1

protective, no assertion criteria provided

literature only

OMIM

May 18, 2015

- -

Systemic lupus erythematosus, susceptibility to

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Apr 27, 2010

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Benign

0.89

DEOGEN2

Benign

0.047

.;.;T

Eigen

Benign

-0.75

Eigen_PC

Benign

-0.76

FATHMM_MKL

Benign

0.043

LIST_S2

Benign

0.68

T;T;T

MetaRNN

Benign

0.0057

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.0

L;.;L

MutationTaster

Benign

1.0

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

PrimateAI

Benign

0.41

PROVEAN

Benign

-1.9

N;N;N

REVEL

Benign

0.024

Sift

Benign

0.22

T;T;T

Sift4G

Benign

0.17

T;T;T

Polyphen

0.10

B;B;B

Vest4

0.10

MPC

0.95

ClinPred

0.0034

GERP RS

2.9

Varity_R

0.029

gMVP

0.24

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