Variant rs812936 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000303225.12(FUT3):c.202C>T(p.Arg68Trp) variant causes a missense change. The variant allele was found at a frequency of 0.83 in 1,594,038 control chromosomes in the GnomAD database, including 546,177 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 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 0.84 ( 51983 hom., cov: 21)

Exomes 𝑓: 0.83 ( 494194 hom. )

Consequence

FUT3
ENST00000303225.12 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.04

Variant links:

Genes affected

FUT3 (HGNC:4014): (fucosyltransferase 3 (Lewis blood group)) The Lewis histo-blood group system comprises a set of fucosylated glycosphingolipids that are synthesized by exocrine epithelial cells and circulate in body fluids. The glycosphingolipids function in embryogenesis, tissue differentiation, tumor metastasis, inflammation, and bacterial adhesion. They are secondarily absorbed to red blood cells giving rise to their Lewis phenotype. This gene is a member of the fucosyltransferase family, which catalyzes the addition of fucose to precursor polysaccharides in the last step of Lewis antigen biosynthesis. It encodes an enzyme with alpha(1,3)-fucosyltransferase and alpha(1,4)-fucosyltransferase activities. Mutations in this gene are responsible for the majority of Lewis antigen-negative phenotypes. Differences in the expression of this gene are associated with host susceptibility to viral infection. [provided by RefSeq, Aug 2020]

FUT3 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=2.923837E-6).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FUT3	NM_001382749.2 linkuse as main transcript	c.202C>T	p.Arg68Trp	missense_variant	3/3		NP_001369678.1
FUT3	NM_001097639.3 linkuse as main transcript	c.202C>T	p.Trp68=	synonymous_variant	3/3	ENST00000709635.1	NP_001091108.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FUT3	ENST00000303225.12 linkuse as main transcript	c.202C>T	p.Arg68Trp	missense_variant	3/3	1		ENSP00000305603	P1

Frequencies

GnomAD3 genomes

AF:

0.837

AC:

123810

AN:

147952

Hom.:

51915

Cov.:

show subpopulations

Gnomad AFR

AF:

0.884

Gnomad AMI

AF:

0.947

Gnomad AMR

AF:

0.851

Gnomad ASJ

AF:

0.752

Gnomad EAS

AF:

0.970

Gnomad SAS

AF:

0.831

Gnomad FIN

AF:

0.801

Gnomad MID

AF:

0.774

Gnomad NFE

AF:

0.806

Gnomad OTH

AF:

0.791

GnomAD3 exomes

AF:

0.830

AC:

208584

AN:

251236

Hom.:

87155

AF XY:

0.824

AC XY:

111937

AN XY:

135826

show subpopulations

Gnomad AFR exome

AF:

0.883

Gnomad AMR exome

AF:

0.895

Gnomad ASJ exome

AF:

0.753

Gnomad EAS exome

AF:

0.972

Gnomad SAS exome

AF:

0.823

Gnomad FIN exome

AF:

0.791

Gnomad NFE exome

AF:

0.798

Gnomad OTH exome

AF:

0.806

GnomAD4 exome

AF:

0.830

AC:

1199882

AN:

1445968

Hom.:

494194

Cov.:

AF XY:

0.828

AC XY:

595474

AN XY:

719432

show subpopulations

Gnomad4 AFR exome

AF:

0.890

Gnomad4 AMR exome

AF:

0.893

Gnomad4 ASJ exome

AF:

0.770

Gnomad4 EAS exome

AF:

0.982

Gnomad4 SAS exome

AF:

0.819

Gnomad4 FIN exome

AF:

0.807

Gnomad4 NFE exome

AF:

0.823

Gnomad4 OTH exome

AF:

0.835

GnomAD4 genome

AF:

0.837

AC:

123937

AN:

148070

Hom.:

51983

Cov.:

AF XY:

0.835

AC XY:

60161

AN XY:

72034

show subpopulations

Gnomad4 AFR

AF:

0.884

Gnomad4 AMR

AF:

0.851

Gnomad4 ASJ

AF:

0.752

Gnomad4 EAS

AF:

0.970

Gnomad4 SAS

AF:

0.831

Gnomad4 FIN

AF:

0.801

Gnomad4 NFE

AF:

0.806

Gnomad4 OTH

AF:

0.795

Alfa

AF:

0.812

Hom.:

98362

Bravo

AF:

0.845

TwinsUK

AF:

0.822

AC:

3049

ALSPAC

AF:

0.821

AC:

3166

ESP6500AA

AF:

0.887

AC:

3910

ESP6500EA

AF:

0.800

AC:

6880

ExAC

AF:

0.828

AC:

100468

Asia WGS

AF:

0.921

AC:

3198

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.017

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.68

CADD

Benign

DANN

Benign

0.60

DEOGEN2

Benign

0.0062

.;.;.;.;.;T

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.019

LIST_S2

Benign

0.28

.;.;.;.;T;T

MetaRNN

Benign

0.0000029

T;T;T;T;T;T

MetaSVM

Benign

-0.96

MutationTaster

Benign

1.0

P;P;P;P

PrimateAI

Uncertain

0.56

PROVEAN

Benign

N;N;.;.;.;.

REVEL

Benign

0.070

Sift

Benign

1.0

T;T;.;.;.;.

Sift4G

Benign

1.0

T;T;T;T;T;T

Vest4

0.064

MPC

0.57

ClinPred

0.0037

GERP RS

2.3

gMVP

0.91

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