Variant chr1-161629785-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001244753.2(FCGR3B):c.312C>A(p.Val104=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 1,431,338 control chromosomes in the GnomAD database, including 1,573 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.011 ( 93 hom., cov: 10)

Exomes 𝑓: 0.010 ( 1480 hom. )

Consequence

FCGR3B
NM_001244753.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.273

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 -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 1-161629785-G-T is Benign according to our data. Variant chr1-161629785-G-T is described in ClinVar as [Benign]. Clinvar id is 2639515.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-161629785-G-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.273 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 93 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCGR3B	NM_001244753.2 linkuse as main transcript	c.312C>A	p.Val104=	synonymous_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.312C>A	p.Val104=	synonymous_variant	3/5		NM_001244753.2	P2

Frequencies

GnomAD3 genomes

AF:

0.0108

AC:

834

AN:

76938

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00291

Gnomad AMI

AF:

0.0372

Gnomad AMR

AF:

0.00859

Gnomad ASJ

AF:

0.00207

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00363

Gnomad FIN

AF:

0.0379

Gnomad MID

AF:

0.00450

Gnomad NFE

AF:

0.0124

Gnomad OTH

AF:

0.0102

GnomAD3 exomes

AF:

0.00920

AC:

2108

AN:

229208

Hom.:

195

AF XY:

0.00922

AC XY:

1152

AN XY:

124954

show subpopulations

Gnomad AFR exome

AF:

0.00177

Gnomad AMR exome

AF:

0.00357

Gnomad ASJ exome

AF:

0.00102

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00339

Gnomad FIN exome

AF:

0.0325

Gnomad NFE exome

AF:

0.0111

Gnomad OTH exome

AF:

0.00739

GnomAD4 exome

AF:

0.0103

AC:

13944

AN:

1354350

Hom.:

1480

Cov.:

AF XY:

0.0102

AC XY:

6825

AN XY:

672076

show subpopulations

Gnomad4 AFR exome

AF:

0.00150

Gnomad4 AMR exome

AF:

0.00410

Gnomad4 ASJ exome

AF:

0.00128

Gnomad4 EAS exome

AF:

0.0000347

Gnomad4 SAS exome

AF:

0.00440

Gnomad4 FIN exome

AF:

0.0320

Gnomad4 NFE exome

AF:

0.0109

Gnomad4 OTH exome

AF:

0.00785

GnomAD4 genome

AF:

0.0108

AC:

832

AN:

76988

Hom.:

Cov.:

AF XY:

0.0112

AC XY:

404

AN XY:

36116

show subpopulations

Gnomad4 AFR

AF:

0.00290

Gnomad4 AMR

AF:

0.00842

Gnomad4 ASJ

AF:

0.00207

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00302

Gnomad4 FIN

AF:

0.0379

Gnomad4 NFE

AF:

0.0124

Gnomad4 OTH

AF:

0.0101

Alfa

AF:

0.00611

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2022

FCGR3B: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

6.9

DANN

Benign

0.72

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