chr14-65561728-A-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001371533.1(FUT8):c.165A>G(p.Gln55Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 1,612,804 control chromosomes in the GnomAD database, including 391,057 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.70 ( 37609 hom., cov: 33)

Exomes 𝑓: 0.69 ( 353448 hom. )

Consequence

FUT8
NM_001371533.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 0.803

Publications

16 publications found

Variant links:

Genes affected

FUT8 (HGNC:4019): (fucosyltransferase 8) This gene encodes an enzyme belonging to the family of fucosyltransferases. The product of this gene catalyzes the transfer of fucose from GDP-fucose to N-linked type complex glycopeptides. This enzyme is distinct from other fucosyltransferases which catalyze alpha1-2, alpha1-3, and alpha1-4 fucose addition. The expression of this gene may contribute to the malignancy of cancer cells and to their invasive and metastatic capabilities. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011]

FUT8 Gene-Disease associations (from GenCC):

congenital disorder of glycosylation with defective fucosylation 1
Inheritance: AR Classification: STRONG, MODERATE Submitted by: PanelApp Australia, Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)

FUT8 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 14-65561728-A-G is Benign according to our data. Variant chr14-65561728-A-G is described in ClinVar as [Benign]. Clinvar id is 402887.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.803 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FUT8	NM_001371533.1 link	c.165A>G	p.Gln55Gln	synonymous_variant	Exon 3 of 11	ENST00000673929.1	NP_001358462.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FUT8	ENST00000673929.1 link	c.165A>G	p.Gln55Gln	synonymous_variant	Exon 3 of 11		NM_001371533.1	ENSP00000501213.1		Q9BYC5-1

Frequencies

GnomAD3 genomes

AF:

0.701

AC:

106415

AN:

151896

Hom.:

37565

Cov.:

show subpopulations

Gnomad AFR

AF:

0.731

Gnomad AMI

AF:

0.726

Gnomad AMR

AF:

0.701

Gnomad ASJ

AF:

0.692

Gnomad EAS

AF:

0.900

Gnomad SAS

AF:

0.775

Gnomad FIN

AF:

0.608

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.677

Gnomad OTH

AF:

0.672

GnomAD2 exomes

AF:

0.705

AC:

176424

AN:

250400

AF XY:

0.704

show subpopulations

Gnomad AFR exome

AF:

0.734

Gnomad AMR exome

AF:

0.704

Gnomad ASJ exome

AF:

0.691

Gnomad EAS exome

AF:

0.902

Gnomad FIN exome

AF:

0.618

Gnomad NFE exome

AF:

0.670

Gnomad OTH exome

AF:

0.677

GnomAD4 exome

AF:

0.694

AC:

1013653

AN:

1460790

Hom.:

353448

Cov.:

AF XY:

0.695

AC XY:

505249

AN XY:

726710

show subpopulations

African (AFR)

AF:

0.726

AC:

24277

AN:

33428

American (AMR)

AF:

0.706

AC:

31510

AN:

44660

Ashkenazi Jewish (ASJ)

AF:

0.687

AC:

17938

AN:

26096

East Asian (EAS)

AF:

0.902

AC:

35784

AN:

39670

South Asian (SAS)

AF:

0.771

AC:

66510

AN:

86228

European-Finnish (FIN)

AF:

0.620

AC:

33115

AN:

53402

Middle Eastern (MID)

AF:

0.633

AC:

3644

AN:

5758

European-Non Finnish (NFE)

AF:

0.682

AC:

758347

AN:

1111208

Other (OTH)

AF:

0.705

AC:

42528

AN:

60340

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

15641

31281

46922

62562

78203

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.701

AC:

106516

AN:

152014

Hom.:

37609

Cov.:

AF XY:

0.702

AC XY:

52161

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.731

AC:

30328

AN:

41478

American (AMR)

AF:

0.701

AC:

10691

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.692

AC:

2401

AN:

3472

East Asian (EAS)

AF:

0.900

AC:

4659

AN:

5178

South Asian (SAS)

AF:

0.774

AC:

3725

AN:

4812

European-Finnish (FIN)

AF:

0.608

AC:

6416

AN:

10544

Middle Eastern (MID)

AF:

0.602

AC:

177

AN:

294

European-Non Finnish (NFE)

AF:

0.677

AC:

46034

AN:

67972

Other (OTH)

AF:

0.675

AC:

1426

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1641

3282

4923

6564

8205

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.685

Hom.:

58466

Bravo

AF:

0.707

Asia WGS

AF:

0.847

AC:

2943

AN:

3476

EpiCase

AF:

0.668

EpiControl

AF:

0.663

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Jun 14, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Congenital disorder of glycosylation with defective fucosylation 1

Benign:1

Aug 10, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

FUT8-related disorder

Benign:1

May 22, 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

BayesDel_noAF

Benign

-0.59

CADD

Benign

7.5

(source)

DANN

Benign

0.56

PhyloP100

0.80

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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chr14-65561728-A-G

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