Variant chr1-161671477-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.219G>A(p.Gly73=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00686 in 1,613,888 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: 𝑓 0.0054 ( 0 hom., cov: 29)

Exomes 𝑓: 0.0070 ( 2 hom. )

Consequence

FCGR2B
NM_001394477.1 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.545

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=-0.84).

BP7

Synonymous conserved (PhyloP=-0.545 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCGR2B	NM_001394477.1 linkuse as main transcript	c.219G>A	p.Gly73=	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.219G>A	p.Gly73=	synonymous_variant	3/8	1	NM_001394477.1	P4	P31994-1

Frequencies

GnomAD3 genomes

AF:

0.00540

AC:

822

AN:

152130

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00128

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.00897

Gnomad ASJ

AF:

0.00893

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00517

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00798

Gnomad OTH

AF:

0.0110

GnomAD3 exomes

AF:

0.00528

AC:

1327

AN:

251438

Hom.:

AF XY:

0.00540

AC XY:

734

AN XY:

135888

show subpopulations

Gnomad AFR exome

AF:

0.000923

Gnomad AMR exome

AF:

0.00448

Gnomad ASJ exome

AF:

0.0136

Gnomad EAS exome

AF:

0.000218

Gnomad SAS exome

AF:

0.00431

Gnomad FIN exome

AF:

0.000370

Gnomad NFE exome

AF:

0.00731

Gnomad OTH exome

AF:

0.00733

GnomAD4 exome

AF:

0.00702

AC:

10258

AN:

1461640

Hom.:

Cov.:

AF XY:

0.00695

AC XY:

5052

AN XY:

727124

show subpopulations

Gnomad4 AFR exome

AF:

0.00149

Gnomad4 AMR exome

AF:

0.00445

Gnomad4 ASJ exome

AF:

0.0113

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.00452

Gnomad4 FIN exome

AF:

0.000543

Gnomad4 NFE exome

AF:

0.00783

Gnomad4 OTH exome

AF:

0.00813

GnomAD4 genome

AF:

0.00539

AC:

821

AN:

152248

Hom.:

Cov.:

AF XY:

0.00517

AC XY:

385

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.00128

Gnomad4 AMR

AF:

0.00896

Gnomad4 ASJ

AF:

0.00893

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00497

Gnomad4 FIN

AF:

0.000377

Gnomad4 NFE

AF:

0.00798

Gnomad4 OTH

AF:

0.0109

Alfa

AF:

0.00783

Hom.:

EpiCase

AF:

0.00992

EpiControl

AF:

0.00890

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

-0.84

CADD

Benign

1.0

DANN

Benign

0.78

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