Genetic Variant NM_001244753.2:c.108C>A (chr1-161629989-G-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001244753.2(FCGR3B):c.108C>A(p.Ser36Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 17)

Exomes 𝑓: 0.0000016 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

FCGR3B
NM_001244753.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01

Publications

21 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 -2 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.08086544).

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
FCGR3B	NM_001244753.2	MANE Select	c.108C>A	p.Ser36Arg	missense	Exon 3 of 5	NP_001231682.2
FCGR3B	NM_000570.5		c.108C>A	p.Ser36Arg	missense	Exon 4 of 6	NP_000561.3
FCGR3B	NM_001271035.2		c.105C>A	p.Ser35Arg	missense	Exon 3 of 5	NP_001257964.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
FCGR3B	ENST00000650385.1	MANE Select	c.108C>A	p.Ser36Arg	missense	Exon 3 of 5	ENSP00000497461.1
ENSG00000289768	ENST00000699402.1		c.40+1066C>A		intron	N/A	ENSP00000514363.1
FCGR3B	ENST00000367964.6	TSL:5	c.108C>A	p.Ser36Arg	missense	Exon 4 of 6	ENSP00000356941.2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

108250

Hom.:

Cov.:

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:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00000960

AC:

AN:

208406

AF XY:

0.00

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:

0.0000200

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00000159

AC:

AN:

1255032

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

623504

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

25938

American (AMR)

AF:

0.00

AC:

AN:

34302

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

23846

East Asian (EAS)

AF:

0.00

AC:

AN:

24980

South Asian (SAS)

AF:

0.00

AC:

AN:

68040

European-Finnish (FIN)

AF:

0.00

AC:

AN:

45538

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5022

European-Non Finnish (NFE)

AF:

0.00000205

AC:

AN:

976126

Other (OTH)

AF:

0.00

AC:

AN:

51240

Age Distribution

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: AC0

AF:

0.00

AC:

AN:

108304

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

52248

African (AFR)

AF:

0.00

AC:

AN:

27226

American (AMR)

AF:

0.00

AC:

AN:

9614

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2922

East Asian (EAS)

AF:

0.00

AC:

AN:

2416

South Asian (SAS)

AF:

0.00

AC:

AN:

2828

European-Finnish (FIN)

AF:

0.00

AC:

AN:

7808

Middle Eastern (MID)

AF:

0.00

AC:

AN:

228

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

53180

Other (OTH)

AF:

0.00

AC:

AN:

1478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.045

BayesDel_addAF

Benign

-0.32

BayesDel_noAF

Benign

-0.69

CADD

Benign

0.15

(source)

DANN

Benign

0.10

DEOGEN2

Benign

0.0034

Eigen

Benign

-1.9

Eigen_PC

Benign

-2.0

FATHMM_MKL

Benign

0.0031

LIST_S2

Benign

0.076

M_CAP

Benign

0.00094

MetaRNN

Benign

0.081

MetaSVM

Benign

-0.97

PhyloP100

-1.0

PrimateAI

Benign

0.35

PROVEAN

Benign

2.2

REVEL

Benign

0.016

Sift

Benign

1.0

Sift4G

Benign

0.52

Vest4

0.17

MutPred

0.40

Loss of ubiquitination at K40 (P = 0.0768)

MVP

0.10

MPC

0.010

ClinPred

0.048

GERP RS

-5.1

gMVP

0.27

Mutation Taster

=97/3

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over