dbSNP rs370893367: FCGR3B:p.Ser97Asn (chr1-161629807-C-T) – ACMG Classification: Likely_benign (-5 pts)

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4BS2

The NM_001244753.2(FCGR3B):c.290G>A(p.Ser97Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000121 in 1,343,142 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000078 ( 1 hom., cov: 10)

Exomes 𝑓: 0.00012 ( 15 hom. )

Failed GnomAD Quality Control

Consequence

FCGR3B
NM_001244753.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.59

Publications

1 publications found

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 Gene-Disease associations (from GenCC):

systemic lupus erythematosus
Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

FCGR3B links:

ENSG00000289768 (HGNC:):

ENSG00000289768 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.28362834).

BS2

High Homozygotes in GnomAdExome4 at 15 Unknown gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001244753.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FCGR3B	NM_001244753.2	MANE Select	c.290G>A	p.Ser97Asn	missense	Exon 3 of 5	NP_001231682.2	A0A3B3ISU3
FCGR3B	NM_000570.5		c.290G>A	p.Ser97Asn	missense	Exon 4 of 6	NP_000561.3	O75015
FCGR3B	NM_001271035.2		c.287G>A	p.Ser96Asn	missense	Exon 3 of 5	NP_001257964.2	H0Y4U3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FCGR3B	ENST00000650385.1	MANE Select	c.290G>A	p.Ser97Asn	missense	Exon 3 of 5	ENSP00000497461.1	A0A3B3ISU3
ENSG00000289768	ENST00000699402.1		c.40+1248G>A		intron	N/A	ENSP00000514363.1	A0A8V8TN80
FCGR3B	ENST00000367964.6	TSL:5	c.290G>A	p.Ser97Asn	missense	Exon 4 of 6	ENSP00000356941.2	O75015

Frequencies

GnomAD3 genomes

AF:

0.0000780

AC:

AN:

76942

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000145

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000798

AC:

AN:

225704

AF XY:

0.000114

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000169

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000121

AC:

162

AN:

1343142

Hom.:

Cov.:

AF XY:

0.000133

AC XY:

AN XY:

667048

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

27516

American (AMR)

AF:

0.0000250

AC:

AN:

39980

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

24834

East Asian (EAS)

AF:

0.00

AC:

AN:

29084

South Asian (SAS)

AF:

0.00

AC:

AN:

74806

European-Finnish (FIN)

AF:

0.00

AC:

AN:

47394

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5248

European-Non Finnish (NFE)

AF:

0.000149

AC:

155

AN:

1039638

Other (OTH)

AF:

0.000110

AC:

AN:

54642

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.557

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000779

AC:

AN:

76990

Hom.:

Cov.:

AF XY:

0.000110

AC XY:

AN XY:

36216

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

17668

American (AMR)

AF:

0.00

AC:

AN:

5824

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2430

East Asian (EAS)

AF:

0.00

AC:

AN:

1636

South Asian (SAS)

AF:

0.00

AC:

AN:

1624

European-Finnish (FIN)

AF:

0.00

AC:

AN:

4788

Middle Eastern (MID)

AF:

0.00

AC:

AN:

202

European-Non Finnish (NFE)

AF:

0.000145

AC:

AN:

41396

Other (OTH)

AF:

0.00

AC:

AN:

994

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000144

Hom.:

ExAC

AF:

0.0000663

AC:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.92

BayesDel_addAF

Benign

-0.11

BayesDel_noAF

Benign

-0.40

CADD

Pathogenic

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.25

Eigen

Uncertain

0.51

Eigen_PC

Uncertain

0.28

FATHMM_MKL

Benign

0.73

LIST_S2

Uncertain

0.90

M_CAP

Benign

0.016

MetaRNN

Benign

0.28

MetaSVM

Benign

-0.90

PhyloP100

3.6

PrimateAI

Uncertain

0.51

PROVEAN

Uncertain

-3.0

REVEL

Benign

0.28

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Vest4

0.47

MVP

0.65

MPC

3.0

ClinPred

0.91

GERP RS

2.8

gMVP

0.57

Mutation Taster

=87/13

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over