19-5844332-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The ENST00000303225.12(FUT3):c.508G>A(p.Gly170Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0465 in 1,613,770 control chromosomes in the GnomAD database, including 5,663 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.11 ( 1744 hom., cov: 31)

Exomes 𝑓: 0.040 ( 3919 hom. )

Consequence

FUT3
ENST00000303225.12 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 4.10

Publications

57 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0018966794).

BP6

Variant 19-5844332-C-T is Benign according to our data. Variant chr19-5844332-C-T is described in ClinVar as Benign. ClinVar VariationId is 242700.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	Protein	UniProt
FUT3	NM_000149.4 link	c.508G>A	p.Gly170Ser	missense_variant	Exon 3 of 3	NP_000140.1	P21217A8K737
FUT3	NM_001097639.3 link	c.508G>A	p.Gly170Ser	missense_variant	Exon 3 of 3	NP_001091108.3	P21217A8K737
FUT3	NM_001097640.3 link	c.508G>A	p.Gly170Ser	missense_variant	Exon 3 of 3	NP_001091109.3	P21217A8K737

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FUT3	ENST00000589620.6 link	c.508G>A	p.Gly170Ser	missense_variant	Exon 3 of 3	1		ENSP00000465804.1		P21217

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16707

AN:

151836

Hom.:

1728

Cov.:

show subpopulations

Gnomad AFR

AF:

0.250

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.191

Gnomad ASJ

AF:

0.0179

Gnomad EAS

AF:

0.168

Gnomad SAS

AF:

0.0618

Gnomad FIN

AF:

0.0664

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0193

Gnomad OTH

AF:

0.0977

GnomAD2 exomes

AF:

0.0851

AC:

21246

AN:

249570

AF XY:

0.0728

show subpopulations

Gnomad AFR exome

AF:

0.256

Gnomad AMR exome

AF:

0.242

Gnomad ASJ exome

AF:

0.0201

Gnomad EAS exome

AF:

0.167

Gnomad FIN exome

AF:

0.0637

Gnomad NFE exome

AF:

0.0199

Gnomad OTH exome

AF:

0.0570

GnomAD4 exome

AF:

0.0398

AC:

58216

AN:

1461816

Hom.:

3919

Cov.:

AF XY:

0.0382

AC XY:

27746

AN XY:

727212

show subpopulations

African (AFR)

AF:

0.255

AC:

8534

AN:

33476

American (AMR)

AF:

0.235

AC:

10524

AN:

44712

Ashkenazi Jewish (ASJ)

AF:

0.0182

AC:

475

AN:

26136

East Asian (EAS)

AF:

0.203

AC:

8055

AN:

39700

South Asian (SAS)

AF:

0.0527

AC:

4543

AN:

86258

European-Finnish (FIN)

AF:

0.0613

AC:

3269

AN:

53362

Middle Eastern (MID)

AF:

0.0156

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.0178

AC:

19831

AN:

1112010

Other (OTH)

AF:

0.0479

AC:

2895

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

3948

7895

11843

15790

19738

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1090

2180

3270

4360

5450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.110

AC:

16744

AN:

151954

Hom.:

1744

Cov.:

AF XY:

0.114

AC XY:

8438

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.250

AC:

10354

AN:

41418

American (AMR)

AF:

0.192

AC:

2929

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.0179

AC:

AN:

3472

East Asian (EAS)

AF:

0.168

AC:

856

AN:

5096

South Asian (SAS)

AF:

0.0614

AC:

296

AN:

4818

European-Finnish (FIN)

AF:

0.0664

AC:

704

AN:

10602

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0193

AC:

1313

AN:

67964

Other (OTH)

AF:

0.0986

AC:

208

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

669

1338

2008

2677

3346

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

166

332

498

664

830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0521

Hom.:

320

Bravo

AF:

0.127

ESP6500AA

AF:

0.247

AC:

1082

ESP6500EA

AF:

0.0172

AC:

147

ExAC

AF:

0.0815

AC:

9889

EpiCase

AF:

0.0148

EpiControl

AF:

0.0152

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

FUT3-related disorder

Benign:1

Oct 18, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.35

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.44

CADD

Benign

(source)

DANN

Uncertain

1.0

Eigen

Uncertain

0.31

Eigen_PC

Benign

0.11

FATHMM_MKL

Uncertain

0.81

MetaRNN

Benign

0.0019

T;T;T;T

MetaSVM

Benign

-1.1

PhyloP100

4.1

PrimateAI

Benign

0.36

PROVEAN

Pathogenic

-5.7

D;D;.;.

REVEL

Benign

0.26

Sift

Uncertain

0.011

D;D;.;.

Sift4G

Pathogenic

0.0

D;D;D;D

Vest4

0.12

MPC

1.4

ClinPred

0.027

GERP RS

2.2

gMVP

0.56

Mutation Taster

=98/2

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over