19-5844781-A-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP6BA1

The NM_001097639.3(FUT3):c.59T>G(p.Leu20Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 1,613,776 control chromosomes in the GnomAD database, including 17,342 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.18 ( 3212 hom., cov: 33)

Exomes 𝑓: 0.12 ( 14130 hom. )

Consequence

FUT3
NM_001097639.3 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.529

Publications

84 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 -11 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.07336402).

BP6

Variant 19-5844781-A-C is Benign according to our data. Variant chr19-5844781-A-C is described in ClinVar as Benign. ClinVar VariationId is 242770.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001097639.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FUT3	NM_001097639.3	MANE Select	c.59T>G	p.Leu20Arg	missense	Exon 3 of 3	NP_001091108.3	A8K737
FUT3	NM_000149.4		c.59T>G	p.Leu20Arg	missense	Exon 3 of 3	NP_000140.1	A8K737
FUT3	NM_001097640.3		c.59T>G	p.Leu20Arg	missense	Exon 3 of 3	NP_001091109.3	A8K737

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FUT3	ENST00000303225.12	TSL:1	c.59T>G	p.Leu20Arg	missense	Exon 3 of 3	ENSP00000305603.5	P21217
FUT3	ENST00000458379.7	TSL:1	c.59T>G	p.Leu20Arg	missense	Exon 2 of 2	ENSP00000416443.1	P21217
FUT3	ENST00000589620.6	TSL:1	c.59T>G	p.Leu20Arg	missense	Exon 3 of 3	ENSP00000465804.1	P21217

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

27548

AN:

152030

Hom.:

3194

Cov.:

show subpopulations

Gnomad AFR

AF:

0.291

Gnomad AMI

AF:

0.0912

Gnomad AMR

AF:

0.258

Gnomad ASJ

AF:

0.150

Gnomad EAS

AF:

0.302

Gnomad SAS

AF:

0.232

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0939

Gnomad OTH

AF:

0.185

GnomAD2 exomes

AF:

0.176

AC:

44047

AN:

250298

AF XY:

0.170

show subpopulations

Gnomad AFR exome

AF:

0.295

Gnomad AMR exome

AF:

0.292

Gnomad ASJ exome

AF:

0.144

Gnomad EAS exome

AF:

0.298

Gnomad FIN exome

AF:

0.136

Gnomad NFE exome

AF:

0.0980

Gnomad OTH exome

AF:

0.153

GnomAD4 exome

AF:

0.122

AC:

177670

AN:

1461628

Hom.:

14130

Cov.:

AF XY:

0.123

AC XY:

89702

AN XY:

727116

show subpopulations

African (AFR)

AF:

0.296

AC:

9903

AN:

33476

American (AMR)

AF:

0.288

AC:

12846

AN:

44636

Ashkenazi Jewish (ASJ)

AF:

0.144

AC:

3768

AN:

26132

East Asian (EAS)

AF:

0.300

AC:

11896

AN:

39692

South Asian (SAS)

AF:

0.235

AC:

20221

AN:

86226

European-Finnish (FIN)

AF:

0.137

AC:

7293

AN:

53386

Middle Eastern (MID)

AF:

0.123

AC:

710

AN:

5768

European-Non Finnish (NFE)

AF:

0.0923

AC:

102674

AN:

1111924

Other (OTH)

AF:

0.138

AC:

8359

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

10196

20393

30589

40786

50982

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4178

8356

12534

16712

20890

<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:

0.181

AC:

27602

AN:

152148

Hom.:

3212

Cov.:

AF XY:

0.187

AC XY:

13927

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.291

AC:

12085

AN:

41488

American (AMR)

AF:

0.259

AC:

3960

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.150

AC:

519

AN:

3470

East Asian (EAS)

AF:

0.301

AC:

1552

AN:

5152

South Asian (SAS)

AF:

0.233

AC:

1125

AN:

4832

European-Finnish (FIN)

AF:

0.137

AC:

1459

AN:

10614

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0939

AC:

6388

AN:

67994

Other (OTH)

AF:

0.189

AC:

400

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1088

2177

3265

4354

5442

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

280

560

840

1120

1400

<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:

0.107

Hom.:

970

Bravo

AF:

0.193

TwinsUK

AF:

0.0982

AC:

364

ALSPAC

AF:

0.0981

AC:

378

ESP6500AA

AF:

0.282

AC:

1244

ESP6500EA

AF:

0.0984

AC:

846

ExAC

AF:

0.173

AC:

21065

Asia WGS

AF:

0.342

AC:

1189

AN:

3478

EpiCase

AF:

0.0978

EpiControl

AF:

0.0963

ClinVar

ClinVar submissions

Significance:Benign

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

FUT3-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.27

BayesDel_addAF

Benign

-0.34

BayesDel_noAF

Benign

-0.11

CADD

Benign

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.097

Eigen

Benign

-0.25

Eigen_PC

Benign

-0.53

FATHMM_MKL

Benign

0.12

LIST_S2

Benign

0.54

MetaRNN

Benign

0.073

MetaSVM

Benign

-1.0

PhyloP100

0.53

PrimateAI

Benign

0.35

PROVEAN

Uncertain

-3.6

REVEL

Benign

0.27

Sift

Benign

0.035

Sift4G

Uncertain

0.0050

Vest4

0.18

MPC

1.8

ClinPred

0.030

GERP RS

2.3

gMVP

0.87

Mutation Taster

=98/2

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over