rs35137471

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001371533.1(FUT8):c.570G>A(p.Leu190=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0237 in 1,613,110 control chromosomes in the GnomAD database, including 909 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.021 ( 69 hom., cov: 32)

Exomes 𝑓: 0.024 ( 840 hom. )

Consequence

FUT8
NM_001371533.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 2.30

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 14-65629579-G-A is Benign according to our data. Variant chr14-65629579-G-A is described in ClinVar as [Benign]. Clinvar id is 402888.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.3 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FUT8	NM_001371533.1 linkuse as main transcript	c.570G>A	p.Leu190=	synonymous_variant	6/11	ENST00000673929.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FUT8	ENST00000673929.1 linkuse as main transcript	c.570G>A	p.Leu190=	synonymous_variant	6/11		NM_001371533.1	P1	Q9BYC5-1

Frequencies

GnomAD3 genomes

AF:

0.0209

AC:

3174

AN:

152104

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00551

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.0746

Gnomad ASJ

AF:

0.0210

Gnomad EAS

AF:

0.000962

Gnomad SAS

AF:

0.0230

Gnomad FIN

AF:

0.0176

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0202

Gnomad OTH

AF:

0.0211

GnomAD3 exomes

AF:

0.0360

AC:

9061

AN:

251380

Hom.:

503

AF XY:

0.0319

AC XY:

4331

AN XY:

135870

show subpopulations

Gnomad AFR exome

AF:

0.00431

Gnomad AMR exome

AF:

0.148

Gnomad ASJ exome

AF:

0.0201

Gnomad EAS exome

AF:

0.000544

Gnomad SAS exome

AF:

0.0235

Gnomad FIN exome

AF:

0.0200

Gnomad NFE exome

AF:

0.0206

Gnomad OTH exome

AF:

0.0261

GnomAD4 exome

AF:

0.0240

AC:

35028

AN:

1460888

Hom.:

840

Cov.:

AF XY:

0.0232

AC XY:

16892

AN XY:

726818

show subpopulations

Gnomad4 AFR exome

AF:

0.00323

Gnomad4 AMR exome

AF:

0.138

Gnomad4 ASJ exome

AF:

0.0214

Gnomad4 EAS exome

AF:

0.000504

Gnomad4 SAS exome

AF:

0.0236

Gnomad4 FIN exome

AF:

0.0188

Gnomad4 NFE exome

AF:

0.0213

Gnomad4 OTH exome

AF:

0.0222

GnomAD4 genome

AF:

0.0209

AC:

3180

AN:

152222

Hom.:

Cov.:

AF XY:

0.0219

AC XY:

1627

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.00549

Gnomad4 AMR

AF:

0.0748

Gnomad4 ASJ

AF:

0.0210

Gnomad4 EAS

AF:

0.000964

Gnomad4 SAS

AF:

0.0232

Gnomad4 FIN

AF:

0.0176

Gnomad4 NFE

AF:

0.0202

Gnomad4 OTH

AF:

0.0209

Alfa

AF:

0.0214

Hom.:

Bravo

AF:

0.0263

EpiCase

AF:

0.0204

EpiControl

AF:

0.0187

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 11, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 25, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

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 -

FUT8-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jun 11, 2019

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

-0.46

Cadd

Benign

7.8

Dann

Benign

0.67

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