Variant chr1-161629781-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong

The NM_001244753.2(FCGR3B):c.316A>G(p.Ile106Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.017 ( 4 hom., cov: 9)

Exomes 𝑓: 0.24 ( 50997 hom. )

Failed GnomAD Quality Control

Consequence

FCGR3B
NM_001244753.2 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: -6.08

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005424112).

BP6

Variant 1-161629781-T-C is Benign according to our data. Variant chr1-161629781-T-C is described in ClinVar as [Benign]. Clinvar id is 402858.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-161629781-T-C is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCGR3B	NM_001244753.2 linkuse as main transcript	c.316A>G	p.Ile106Val	missense_variant	3/5	ENST00000650385.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCGR3B	ENST00000650385.1 linkuse as main transcript	c.316A>G	p.Ile106Val	missense_variant	3/5		NM_001244753.2	P2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

1082

AN:

65610

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00925

Gnomad AMI

AF:

0.0255

Gnomad AMR

AF:

0.0243

Gnomad ASJ

AF:

0.00806

Gnomad EAS

AF:

0.0797

Gnomad SAS

AF:

0.0241

Gnomad FIN

AF:

0.00621

Gnomad MID

AF:

0.0278

Gnomad NFE

AF:

0.0181

Gnomad OTH

AF:

0.0239

GnomAD3 exomes

AF:

0.267

AC:

51655

AN:

193734

Hom.:

10600

AF XY:

0.272

AC XY:

28944

AN XY:

106472

show subpopulations

Gnomad AFR exome

AF:

0.154

Gnomad AMR exome

AF:

0.388

Gnomad ASJ exome

AF:

0.196

Gnomad EAS exome

AF:

0.479

Gnomad SAS exome

AF:

0.345

Gnomad FIN exome

AF:

0.180

Gnomad NFE exome

AF:

0.225

Gnomad OTH exome

AF:

0.221

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.239

AC:

288026

AN:

1202724

Hom.:

50997

Cov.:

AF XY:

0.233

AC XY:

139154

AN XY:

596090

show subpopulations

Gnomad4 AFR exome

AF:

0.172

Gnomad4 AMR exome

AF:

0.395

Gnomad4 ASJ exome

AF:

0.146

Gnomad4 EAS exome

AF:

0.285

Gnomad4 SAS exome

AF:

0.242

Gnomad4 FIN exome

AF:

0.0948

Gnomad4 NFE exome

AF:

0.245

Gnomad4 OTH exome

AF:

0.208

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0165

AC:

1084

AN:

65648

Hom.:

Cov.:

AF XY:

0.0151

AC XY:

471

AN XY:

31148

show subpopulations

Gnomad4 AFR

AF:

0.00935

Gnomad4 AMR

AF:

0.0243

Gnomad4 ASJ

AF:

0.00806

Gnomad4 EAS

AF:

0.0787

Gnomad4 SAS

AF:

0.0241

Gnomad4 FIN

AF:

0.00621

Gnomad4 NFE

AF:

0.0181

Gnomad4 OTH

AF:

0.0248

Alfa

AF:

0.160

Hom.:

490

ExAC

AF:

0.349

AC:

42050

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: ExAC frequency -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.079

BayesDel_addAF

Benign

-0.38

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.0010

DANN

Benign

0.46

DEOGEN2

Benign

0.0021

.;.;T;.;.;.;T

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.00071

LIST_S2

Benign

0.14

.;.;T;T;T;T;T

MetaRNN

Benign

0.0054

T;T;T;T;T;T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

P;P;P;P;P;P;P;P

PrimateAI

Benign

0.26

PROVEAN

Benign

0.22

.;N;.;.;N;N;N

REVEL

Benign

0.010

Sift

Benign

0.58

.;T;.;.;T;T;T

Sift4G

Benign

0.22

.;T;T;T;T;T;.

Vest4

0.080, 0.082, 0.084, 0.032, 0.049

MPC

1.5

ClinPred

0.0052

GERP RS

-5.6

gMVP

0.21

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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