Variant chr1-161671447-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2

The NM_001394477.1(FCGR2B):c.189G>A(p.Gln63=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00618 in 1,603,124 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: 𝑓 0.0064 ( 0 hom., cov: 29)

Exomes 𝑓: 0.0062 ( 4 hom. )

Consequence

FCGR2B
NM_001394477.1 synonymous

Scores

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: 0.746

Variant links:

Genes affected

FCGR2B (HGNC:3618): (Fc gamma receptor IIb) The protein encoded by this gene is a low affinity receptor for the Fc region of immunoglobulin gamma complexes. The encoded protein is involved in the phagocytosis of immune complexes and in the regulation of antibody production by B-cells. Variations in this gene may increase susceptibilty to systemic lupus erythematosus (SLE). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]

FCGR2B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP7

Synonymous conserved (PhyloP=0.746 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCGR2B	NM_001394477.1 linkuse as main transcript	c.189G>A	p.Gln63=	synonymous_variant	3/8	ENST00000358671.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCGR2B	ENST00000358671.10 linkuse as main transcript	c.189G>A	p.Gln63=	synonymous_variant	3/8	1	NM_001394477.1	P4	P31994-1

Frequencies

GnomAD3 genomes

AF:

0.00641

AC:

973

AN:

151796

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00212

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.00841

Gnomad ASJ

AF:

0.0145

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00768

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.0129

Gnomad NFE

AF:

0.00940

Gnomad OTH

AF:

0.00962

GnomAD3 exomes

AF:

0.00278

AC:

693

AN:

249478

Hom.:

AF XY:

0.00277

AC XY:

373

AN XY:

134726

show subpopulations

Gnomad AFR exome

AF:

0.00136

Gnomad AMR exome

AF:

0.00281

Gnomad ASJ exome

AF:

0.00478

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00221

Gnomad FIN exome

AF:

0.000416

Gnomad NFE exome

AF:

0.00374

Gnomad OTH exome

AF:

0.00477

GnomAD4 exome

AF:

0.00615

AC:

8928

AN:

1451206

Hom.:

Cov.:

AF XY:

0.00618

AC XY:

4459

AN XY:

721994

show subpopulations

Gnomad4 AFR exome

AF:

0.00179

Gnomad4 AMR exome

AF:

0.00366

Gnomad4 ASJ exome

AF:

0.0105

Gnomad4 EAS exome

AF:

0.000227

Gnomad4 SAS exome

AF:

0.00533

Gnomad4 FIN exome

AF:

0.000880

Gnomad4 NFE exome

AF:

0.00672

Gnomad4 OTH exome

AF:

0.00729

GnomAD4 genome

AF:

0.00641

AC:

974

AN:

151918

Hom.:

Cov.:

AF XY:

0.00598

AC XY:

444

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.00212

Gnomad4 AMR

AF:

0.00840

Gnomad4 ASJ

AF:

0.0145

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00809

Gnomad4 FIN

AF:

0.000377

Gnomad4 NFE

AF:

0.00940

Gnomad4 OTH

AF:

0.00904

Alfa

AF:

0.00904

Hom.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Uncertain:2

Uncertain significance, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

7.0

DANN

Benign

0.66

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

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