Genetic Variant FCGR3B:p.Ala78Val (chr1-161629864-G-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001244753.2(FCGR3B):c.233C>T(p.Ala78Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000135 in 1,405,640 control chromosomes in the GnomAD database, including 1 homozygotes. 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: not found (cov: 10)

Exomes 𝑓: 0.000014 ( 1 hom. )

Consequence

FCGR3B
NM_001244753.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.01

Publications

27 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:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.16208252).

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.233C>T	p.Ala78Val	missense	Exon 3 of 5	NP_001231682.2
FCGR3B	NM_000570.5		c.233C>T	p.Ala78Val	missense	Exon 4 of 6	NP_000561.3
FCGR3B	NM_001271035.2		c.230C>T	p.Ala77Val	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.233C>T	p.Ala78Val	missense	Exon 3 of 5	ENSP00000497461.1
ENSG00000289768	ENST00000699402.1		c.40+1191C>T		intron	N/A	ENSP00000514363.1
FCGR3B	ENST00000367964.6	TSL:5	c.233C>T	p.Ala78Val	missense	Exon 4 of 6	ENSP00000356941.2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.0000135

AC:

AN:

1405640

Hom.:

Cov.:

AF XY:

0.0000143

AC XY:

AN XY:

698118

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

29792

American (AMR)

AF:

0.00

AC:

AN:

42128

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25194

East Asian (EAS)

AF:

0.00

AC:

AN:

31542

South Asian (SAS)

AF:

0.00

AC:

AN:

80836

European-Finnish (FIN)

AF:

0.00

AC:

AN:

49466

Middle Eastern (MID)

AF:

0.000184

AC:

AN:

5442

European-Non Finnish (NFE)

AF:

0.0000148

AC:

AN:

1084126

Other (OTH)

AF:

0.0000350

AC:

AN:

57114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.522

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

185

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.30

BayesDel_noAF

Benign

-0.66

CADD

Benign

0.059

(source)

DANN

Benign

0.95

DEOGEN2

Benign

0.030

Eigen

Benign

-1.0

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.0065

LIST_S2

Benign

0.30

M_CAP

Benign

0.0016

MetaRNN

Benign

0.16

MetaSVM

Benign

-0.99

PhyloP100

-2.0

PrimateAI

Benign

0.29

PROVEAN

Benign

-2.1

REVEL

Benign

0.039

Sift

Benign

0.13

Sift4G

Benign

0.18

Vest4

0.11

MutPred

0.36

Loss of loop (P = 0.1242)

MVP

0.13

MPC

1.7

ClinPred

0.15

GERP RS

-4.0

gMVP

0.20

Mutation Taster

=91/9

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over