Variant 1-157544301-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_031281.3(FCRL5):c.805G>A(p.Val269Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 1,613,592 control chromosomes in the GnomAD database, including 36,126 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.23 ( 4061 hom., cov: 32)

Exomes 𝑓: 0.21 ( 32065 hom. )

Consequence

FCRL5
NM_031281.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.22

Variant links:

Genes affected

FCRL5 (HGNC:18508): (Fc receptor like 5) This gene encodes a member of the immunoglobulin receptor superfamily and the Fc-receptor like family. This gene and several other Fc receptor-like gene members are clustered on the long arm of chromosome 1. The encoded protein is a single-pass type I membrane protein and contains 8 immunoglobulin-like C2-type domains. This gene is implicated in B cell development and lymphomagenesis. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Sep 2010]

FCRL5 links:

FCRL5 (HGNC:):

FCRL5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0034855008).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCRL5	NM_031281.3 linkuse as main transcript	c.805G>A	p.Val269Ile	missense_variant	5/17	ENST00000361835.8	NP_112571.2	Q96RD9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
FCRL5	ENST00000361835.8 linkuse as main transcript	c.805G>A	p.Val269Ile	missense_variant	5/17	1	NM_031281.3	ENSP00000354691.3	Q96RD9-1
FCRL5	ENST00000368190.7 linkuse as main transcript	c.805G>A	p.Val269Ile	missense_variant	5/10	1		ENSP00000357173.3	Q96RD9-3
FCRL5	ENST00000368189.3 linkuse as main transcript	c.805G>A	p.Val269Ile	missense_variant	5/8	1		ENSP00000357172.3	Q96RD9-4
FCRL5	ENST00000481082.1 linkuse as main transcript	n.1003G>A		non_coding_transcript_exon_variant	6/7	2

Frequencies

GnomAD3 genomes

AF:

0.226

AC:

34349

AN:

152032

Hom.:

4064

Cov.:

show subpopulations

Gnomad AFR

AF:

0.294

Gnomad AMI

AF:

0.252

Gnomad AMR

AF:

0.184

Gnomad ASJ

AF:

0.235

Gnomad EAS

AF:

0.0830

Gnomad SAS

AF:

0.159

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.210

Gnomad OTH

AF:

0.252

GnomAD3 exomes

AF:

0.189

AC:

47581

AN:

251146

Hom.:

4898

AF XY:

0.191

AC XY:

25857

AN XY:

135716

show subpopulations

Gnomad AFR exome

AF:

0.297

Gnomad AMR exome

AF:

0.131

Gnomad ASJ exome

AF:

0.228

Gnomad EAS exome

AF:

0.0849

Gnomad SAS exome

AF:

0.177

Gnomad FIN exome

AF:

0.195

Gnomad NFE exome

AF:

0.207

Gnomad OTH exome

AF:

0.198

GnomAD4 exome

AF:

0.206

AC:

300463

AN:

1461442

Hom.:

32065

Cov.:

AF XY:

0.205

AC XY:

148855

AN XY:

727034

show subpopulations

Gnomad4 AFR exome

AF:

0.297

Gnomad4 AMR exome

AF:

0.134

Gnomad4 ASJ exome

AF:

0.225

Gnomad4 EAS exome

AF:

0.0781

Gnomad4 SAS exome

AF:

0.177

Gnomad4 FIN exome

AF:

0.197

Gnomad4 NFE exome

AF:

0.212

Gnomad4 OTH exome

AF:

0.213

GnomAD4 genome

AF:

0.226

AC:

34359

AN:

152150

Hom.:

4061

Cov.:

AF XY:

0.221

AC XY:

16414

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.294

Gnomad4 AMR

AF:

0.184

Gnomad4 ASJ

AF:

0.235

Gnomad4 EAS

AF:

0.0828

Gnomad4 SAS

AF:

0.160

Gnomad4 FIN

AF:

0.209

Gnomad4 NFE

AF:

0.210

Gnomad4 OTH

AF:

0.253

Alfa

AF:

0.203

Hom.:

1861

Bravo

AF:

0.227

TwinsUK

AF:

0.226

AC:

837

ALSPAC

AF:

0.221

AC:

852

ESP6500AA

AF:

0.294

AC:

1295

ESP6500EA

AF:

0.214

AC:

1842

ExAC

AF:

0.192

AC:

23339

Asia WGS

AF:

0.156

AC:

545

AN:

3478

EpiCase

AF:

0.218

EpiControl

AF:

0.223

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.074

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.028

DANN

Benign

0.75

DEOGEN2

Benign

0.0026

T;.;.

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.0037

LIST_S2

Benign

0.26

T;T;T

MetaRNN

Benign

0.0035

T;T;T

MetaSVM

Benign

-0.91

MutationAssessor

Benign

0.68

N;N;N

PrimateAI

Benign

0.36

PROVEAN

Benign

-0.37

N;N;N

REVEL

Benign

0.023

Sift

Benign

0.69

T;T;T

Sift4G

Benign

0.47

T;T;T

Polyphen

0.045

B;B;B

Vest4

0.023

MPC

0.061

ClinPred

0.0015

GERP RS

-1.6

Varity_R

0.011

gMVP

0.089

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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