Variant 1-161675262-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001394477.1(FCGR2B):c.766C>T(p.Pro256Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00671 in 1,599,402 control chromosomes in the GnomAD database, including 229 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.027 ( 140 hom., cov: 31)

Exomes 𝑓: 0.0046 ( 89 hom. )

Consequence

FCGR2B
NM_001394477.1 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.600

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:

FCGR2B (HGNC:):

FCGR2B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.003109455).

BP6

Variant 1-161675262-C-T is Benign according to our data. Variant chr1-161675262-C-T is described in ClinVar as [Benign]. Clinvar id is 779299.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCGR2B	NM_001394477.1 linkuse as main transcript	c.766C>T	p.Pro256Ser	missense_variant	6/8	ENST00000358671.10	NP_001381406.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
FCGR2B	ENST00000358671.10 linkuse as main transcript	c.766C>T	p.Pro256Ser	missense_variant	6/8	1	NM_001394477.1	ENSP00000351497.5	P31994-1
FCGR2B	ENST00000367961.8 linkuse as main transcript	c.745C>T	p.Pro249Ser	missense_variant	5/7	1		ENSP00000356938.4	P31994-3
FCGR2B	ENST00000236937.13 linkuse as main transcript	c.760+1189C>T		intron_variant		1		ENSP00000236937.9	P31994-2
FCGR2B	ENST00000480308.5 linkuse as main transcript	n.1999C>T		non_coding_transcript_exon_variant	5/6	1

Frequencies

GnomAD3 genomes

AF:

0.0271

AC:

4113

AN:

151984

Hom.:

138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0821

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.0143

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00621

Gnomad FIN

AF:

0.00292

Gnomad MID

AF:

0.0191

Gnomad NFE

AF:

0.00543

Gnomad OTH

AF:

0.0192

GnomAD3 exomes

AF:

0.00559

AC:

1353

AN:

241958

Hom.:

AF XY:

0.00475

AC XY:

622

AN XY:

130988

show subpopulations

Gnomad AFR exome

AF:

0.0436

Gnomad AMR exome

AF:

0.00607

Gnomad ASJ exome

AF:

0.00142

Gnomad EAS exome

AF:

0.000509

Gnomad SAS exome

AF:

0.00310

Gnomad FIN exome

AF:

0.00270

Gnomad NFE exome

AF:

0.00270

Gnomad OTH exome

AF:

0.00829

GnomAD4 exome

AF:

0.00457

AC:

6611

AN:

1447300

Hom.:

Cov.:

AF XY:

0.00429

AC XY:

3085

AN XY:

719868

show subpopulations

Gnomad4 AFR exome

AF:

0.0566

Gnomad4 AMR exome

AF:

0.00700

Gnomad4 ASJ exome

AF:

0.00220

Gnomad4 EAS exome

AF:

0.000358

Gnomad4 SAS exome

AF:

0.00383

Gnomad4 FIN exome

AF:

0.00394

Gnomad4 NFE exome

AF:

0.00312

Gnomad4 OTH exome

AF:

0.00752

GnomAD4 genome

AF:

0.0271

AC:

4125

AN:

152102

Hom.:

140

Cov.:

AF XY:

0.0266

AC XY:

1977

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.0822

Gnomad4 AMR

AF:

0.0143

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00601

Gnomad4 FIN

AF:

0.00292

Gnomad4 NFE

AF:

0.00543

Gnomad4 OTH

AF:

0.0190

Alfa

AF:

0.0135

Hom.:

Bravo

AF:

0.0301

ExAC

AF:

0.00619

AC:

752

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 23, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.61

CADD

Benign

0.19

DANN

Uncertain

0.99

DEOGEN2

Benign

0.062

.;T

Eigen

Benign

-0.94

Eigen_PC

Benign

-0.90

FATHMM_MKL

Benign

0.025

LIST_S2

Benign

0.44

T;T

MetaRNN

Benign

0.0031

T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

1.0

.;L

PrimateAI

Benign

0.23

PROVEAN

Benign

-1.1

N;N

REVEL

Benign

0.016

Sift

Benign

0.20

T;T

Sift4G

Benign

0.62

T;T

Polyphen

0.30

B;B

Vest4

0.083

MVP

0.12

MPC

0.76

ClinPred

0.010

GERP RS

1.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.032

gMVP

0.18

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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