Variant rs34868416 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001002901.4(FCRLB):c.1148G>A(p.Gly383Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0802 in 1,614,042 control chromosomes in the GnomAD database, including 5,569 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.062 ( 381 hom., cov: 31)

Exomes 𝑓: 0.082 ( 5188 hom. )

Consequence

FCRLB
NM_001002901.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.21

Variant links:

Genes affected

FCRLB (HGNC:26431): (Fc receptor like B) FCRL2 belongs to the Fc receptor family. Fc receptors are involved in phagocytosis, antibody-dependent cell cytotoxicity, immediate hypersensitivity, and transcytosis of immunoglobulins via their ability to bind immunoglobulin (Ig) constant regions (Chikaev et al., 2005 [PubMed 15676285]).[supplied by OMIM, Mar 2008]

FCRLB 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=0.0016637743).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCRLB	NM_001002901.4 linkuse as main transcript	c.1148G>A	p.Gly383Asp	missense_variant	8/8	ENST00000367948.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCRLB	ENST00000367948.7 linkuse as main transcript	c.1148G>A	p.Gly383Asp	missense_variant	8/8	1	NM_001002901.4	P1	Q6BAA4-1

Frequencies

GnomAD3 genomes

AF:

0.0618

AC:

9401

AN:

152038

Hom.:

380

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0175

Gnomad AMI

AF:

0.0186

Gnomad AMR

AF:

0.0682

Gnomad ASJ

AF:

0.0715

Gnomad EAS

AF:

0.0789

Gnomad SAS

AF:

0.0511

Gnomad FIN

AF:

0.0708

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0854

Gnomad OTH

AF:

0.0690

GnomAD3 exomes

AF:

0.0734

AC:

18377

AN:

250496

Hom.:

761

AF XY:

0.0734

AC XY:

9959

AN XY:

135706

show subpopulations

Gnomad AFR exome

AF:

0.0160

Gnomad AMR exome

AF:

0.0743

Gnomad ASJ exome

AF:

0.0764

Gnomad EAS exome

AF:

0.0776

Gnomad SAS exome

AF:

0.0490

Gnomad FIN exome

AF:

0.0695

Gnomad NFE exome

AF:

0.0872

Gnomad OTH exome

AF:

0.0802

GnomAD4 exome

AF:

0.0821

AC:

120033

AN:

1461886

Hom.:

5188

Cov.:

AF XY:

0.0808

AC XY:

58776

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.0144

Gnomad4 AMR exome

AF:

0.0727

Gnomad4 ASJ exome

AF:

0.0716

Gnomad4 EAS exome

AF:

0.0974

Gnomad4 SAS exome

AF:

0.0486

Gnomad4 FIN exome

AF:

0.0733

Gnomad4 NFE exome

AF:

0.0878

Gnomad4 OTH exome

AF:

0.0750

GnomAD4 genome

AF:

0.0618

AC:

9397

AN:

152156

Hom.:

381

Cov.:

AF XY:

0.0611

AC XY:

4543

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.0174

Gnomad4 AMR

AF:

0.0681

Gnomad4 ASJ

AF:

0.0715

Gnomad4 EAS

AF:

0.0792

Gnomad4 SAS

AF:

0.0508

Gnomad4 FIN

AF:

0.0708

Gnomad4 NFE

AF:

0.0854

Gnomad4 OTH

AF:

0.0682

Alfa

AF:

0.0806

Hom.:

851

Bravo

AF:

0.0611

TwinsUK

AF:

0.0914

AC:

339

ALSPAC

AF:

0.0991

AC:

382

ESP6500AA

AF:

0.0161

AC:

ESP6500EA

AF:

0.0883

AC:

759

ExAC

AF:

0.0713

AC:

8659

Asia WGS

AF:

0.0800

AC:

276

AN:

3478

EpiCase

AF:

0.0833

EpiControl

AF:

0.0847

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.095

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.58

Cadd

Benign

Dann

Uncertain

1.0

DEOGEN2

Benign

0.048

Eigen

Benign

0.074

Eigen_PC

Benign

0.027

FATHMM_MKL

Benign

0.53

LIST_S2

Benign

0.52

MetaRNN

Benign

0.0017

MetaSVM

Benign

-0.81

MutationAssessor

Uncertain

2.1

MutationTaster

Benign

0.74

P;P;P;P;P;P

PrimateAI

Benign

0.41

PROVEAN

Benign

-1.7

REVEL

Benign

0.080

Sift

Benign

0.056

Sift4G

Benign

0.16

Polyphen

0.96

Vest4

0.072

MPC

0.99

ClinPred

0.073

GERP RS

2.4

Varity_R

0.19

gMVP

0.48

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over