Variant chr19-5831829-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_000150.4(FUT6):c.739G>A(p.Glu247Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0621 in 1,613,460 control chromosomes in the GnomAD database, including 5,872 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.12 ( 1889 hom., cov: 31)

Exomes 𝑓: 0.056 ( 3983 hom. )

Consequence

FUT6
NM_000150.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1O:1

Conservation

PhyloP100: 2.27

Variant links:

Genes affected

FUT6 (HGNC:4017): (fucosyltransferase 6) The protein encoded by this gene is a Golgi stack membrane protein that is involved in the creation of sialyl-Lewis X, an E-selectin ligand. Mutations in this gene are a cause of fucosyltransferase-6 deficiency. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

FUT6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0040969253).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FUT6	NM_000150.4 linkuse as main transcript	c.739G>A	p.Glu247Lys	missense_variant	3/3	ENST00000318336.10	NP_000141.1	P51993-1Q6P7E6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FUT6	ENST00000318336.10 linkuse as main transcript	c.739G>A	p.Glu247Lys	missense_variant	3/3	2	NM_000150.4	ENSP00000313398.4		P51993-1

Frequencies

GnomAD3 genomes

AF:

0.117

AC:

17761

AN:

151696

Hom.:

1884

Cov.:

show subpopulations

Gnomad AFR

AF:

0.294

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.0650

Gnomad ASJ

AF:

0.0663

Gnomad EAS

AF:

0.103

Gnomad SAS

AF:

0.137

Gnomad FIN

AF:

0.0290

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0400

Gnomad OTH

AF:

0.104

GnomAD3 exomes

AF:

0.0775

AC:

19475

AN:

251182

Hom.:

1372

AF XY:

0.0776

AC XY:

10540

AN XY:

135756

show subpopulations

Gnomad AFR exome

AF:

0.301

Gnomad AMR exome

AF:

0.0419

Gnomad ASJ exome

AF:

0.0649

Gnomad EAS exome

AF:

0.103

Gnomad SAS exome

AF:

0.155

Gnomad FIN exome

AF:

0.0277

Gnomad NFE exome

AF:

0.0428

Gnomad OTH exome

AF:

0.0643

GnomAD4 exome

AF:

0.0564

AC:

82396

AN:

1461646

Hom.:

3983

Cov.:

AF XY:

0.0584

AC XY:

42488

AN XY:

727132

show subpopulations

Gnomad4 AFR exome

AF:

0.301

Gnomad4 AMR exome

AF:

0.0445

Gnomad4 ASJ exome

AF:

0.0677

Gnomad4 EAS exome

AF:

0.0715

Gnomad4 SAS exome

AF:

0.148

Gnomad4 FIN exome

AF:

0.0294

Gnomad4 NFE exome

AF:

0.0420

Gnomad4 OTH exome

AF:

0.0733

GnomAD4 genome

AF:

0.117

AC:

17806

AN:

151814

Hom.:

1889

Cov.:

AF XY:

0.116

AC XY:

8605

AN XY:

74184

show subpopulations

Gnomad4 AFR

AF:

0.294

Gnomad4 AMR

AF:

0.0648

Gnomad4 ASJ

AF:

0.0663

Gnomad4 EAS

AF:

0.103

Gnomad4 SAS

AF:

0.137

Gnomad4 FIN

AF:

0.0290

Gnomad4 NFE

AF:

0.0400

Gnomad4 OTH

AF:

0.107

Alfa

AF:

0.0766

Hom.:

390

Bravo

AF:

0.127

ESP6500AA

AF:

0.289

AC:

1273

ESP6500EA

AF:

0.0453

AC:

389

ExAC

AF:

0.0833

AC:

10117

Asia WGS

AF:

0.188

AC:

652

AN:

3478

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1Other:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Fucosyltransferase 6 deficiency

Uncertain:1Other:1

Uncertain significance, criteria provided, single submitter	reference population	Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center	Mar 18, 2016	- -
Affects, no assertion criteria provided	literature only	OMIM	Apr 29, 1994	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.93

BayesDel_addAF

Benign

-0.21

BayesDel_noAF

Uncertain

0.070

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.28

T;T;T;T;.

Eigen

Uncertain

0.36

Eigen_PC

Benign

0.11

FATHMM_MKL

Uncertain

0.88

LIST_S2

Benign

0.82

.;.;T;.;T

MetaRNN

Benign

0.0041

T;T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Pathogenic

4.2

H;H;H;H;H

PrimateAI

Uncertain

0.56

PROVEAN

Uncertain

-3.9

D;D;D;D;.

REVEL

Uncertain

0.49

Sift

Uncertain

0.015

D;D;D;D;.

Sift4G

Pathogenic

0.0

D;D;D;D;D

Polyphen

0.92

P;P;P;P;.

Vest4

0.38

MPC

0.58

ClinPred

0.074

GERP RS

2.0

Varity_R

0.71

gMVP

0.78

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over