Genetic Variant NM_001244753.2:c.206G>A (chr1-161629891-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001244753.2(FCGR3B):c.206G>A(p.Ser69Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000023 ( 0 hom., cov: 11)

Exomes 𝑓: 0.000012 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

FCGR3B
NM_001244753.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.84

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 -2 ACMG points.

BP6

Variant 1-161629891-C-T is Benign according to our data. Variant chr1-161629891-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3278340.Status of the report is criteria_provided_single_submitter, 1 stars.

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.206G>A	p.Ser69Asn	missense	Exon 3 of 5	NP_001231682.2	A0A3B3ISU3
FCGR3B	NM_000570.5		c.206G>A	p.Ser69Asn	missense	Exon 4 of 6	NP_000561.3	O75015
FCGR3B	NM_001271035.2		c.203G>A	p.Ser68Asn	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.206G>A	p.Ser69Asn	missense	Exon 3 of 5	ENSP00000497461.1	A0A3B3ISU3
ENSG00000289768	ENST00000699402.1		c.40+1164G>A		intron	N/A	ENSP00000514363.1	A0A8V8TN80
FCGR3B	ENST00000367964.6	TSL:5	c.206G>A	p.Ser69Asn	missense	Exon 4 of 6	ENSP00000356941.2	O75015

Frequencies

GnomAD3 genomes

AF:

0.0000232

AC:

AN:

86364

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:

0.0000435

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00000404

AC:

AN:

247508

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:

0.00000888

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000120

AC:

AN:

1413416

Hom.:

Cov.:

AF XY:

0.0000128

AC XY:

AN XY:

702276

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

30520

American (AMR)

AF:

0.00

AC:

AN:

42426

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25292

East Asian (EAS)

AF:

0.00

AC:

AN:

31802

South Asian (SAS)

AF:

0.00

AC:

AN:

82334

European-Finnish (FIN)

AF:

0.00

AC:

AN:

49902

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5556

European-Non Finnish (NFE)

AF:

0.0000147

AC:

AN:

1088074

Other (OTH)

AF:

0.0000174

AC:

AN:

57510

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.443

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

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000232

AC:

AN:

86364

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

40622

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

19744

American (AMR)

AF:

0.00

AC:

AN:

6836

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2620

East Asian (EAS)

AF:

0.00

AC:

AN:

1982

South Asian (SAS)

AF:

0.00

AC:

AN:

1974

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5410

Middle Eastern (MID)

AF:

0.00

AC:

AN:

238

European-Non Finnish (NFE)

AF:

0.0000435

AC:

AN:

45926

Other (OTH)

AF:

0.00

AC:

AN:

1122

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

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:

0.00

Hom.:

Bravo

AF:

0.00000378

ExAC

AF:

0.00000827

AC:

ClinVar

ClinVar submissions

Significance:Likely benign

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

Benign

0.087

BayesDel_addAF

Benign

-0.38

BayesDel_noAF

Benign

-0.79

CADD

Benign

0.056

(source)

DANN

Benign

0.83

DEOGEN2

Benign

0.0098

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.0021

LIST_S2

Benign

0.57

M_CAP

Benign

0.0013

MetaRNN

Benign

0.053

MetaSVM

Benign

-0.95

PhyloP100

-2.8

PrimateAI

Benign

0.30

PROVEAN

Benign

-0.63

REVEL

Benign

0.010

Sift

Benign

0.13

Sift4G

Benign

0.28

Vest4

0.091

MutPred

0.22

Loss of disorder (P = 0.0966)

MVP

0.22

MPC

1.6

ClinPred

0.050

GERP RS

-3.7

gMVP

0.13

Mutation Taster

=86/14

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.23

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.23

Position offset: -5

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