Variant 14-65561787-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001371533.1(FUT8):c.203+21T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 1,579,590 control chromosomes in the GnomAD database, including 382,627 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.70 ( 37619 hom., cov: 32)

Exomes 𝑓: 0.69 ( 345008 hom. )

Consequence

FUT8
NM_001371533.1 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0890

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:

FUT8 (HGNC:):

FUT8 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 14-65561787-T-C is Benign according to our data. Variant chr14-65561787-T-C is described in ClinVar as [Benign]. Clinvar id is 1238047.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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/exons	MANE	Protein	UniProt
FUT8	NM_001371533.1 linkuse as main transcript	c.203+21T>C		intron_variant		ENST00000673929.1	NP_001358462.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FUT8	ENST00000673929.1 linkuse as main transcript	c.203+21T>C		intron_variant			NM_001371533.1	ENSP00000501213.1		Q9BYC5-1

Frequencies

GnomAD3 genomes

AF:

0.701

AC:

106416

AN:

151884

Hom.:

37575

Cov.:

show subpopulations

Gnomad AFR

AF:

0.731

Gnomad AMI

AF:

0.727

Gnomad AMR

AF:

0.701

Gnomad ASJ

AF:

0.692

Gnomad EAS

AF:

0.900

Gnomad SAS

AF:

0.775

Gnomad FIN

AF:

0.609

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.677

Gnomad OTH

AF:

0.671

GnomAD3 exomes

AF:

0.705

AC:

174678

AN:

247886

Hom.:

62174

AF XY:

0.704

AC XY:

94325

AN XY:

134076

show subpopulations

Gnomad AFR exome

AF:

0.734

Gnomad AMR exome

AF:

0.704

Gnomad ASJ exome

AF:

0.690

Gnomad EAS exome

AF:

0.902

Gnomad SAS exome

AF:

0.769

Gnomad FIN exome

AF:

0.618

Gnomad NFE exome

AF:

0.670

Gnomad OTH exome

AF:

0.677

GnomAD4 exome

AF:

0.693

AC:

989848

AN:

1427588

Hom.:

345008

Cov.:

AF XY:

0.695

AC XY:

494892

AN XY:

712242

show subpopulations

Gnomad4 AFR exome

AF:

0.726

Gnomad4 AMR exome

AF:

0.706

Gnomad4 ASJ exome

AF:

0.687

Gnomad4 EAS exome

AF:

0.902

Gnomad4 SAS exome

AF:

0.771

Gnomad4 FIN exome

AF:

0.620

Gnomad4 NFE exome

AF:

0.682

Gnomad4 OTH exome

AF:

0.704

GnomAD4 genome

AF:

0.701

AC:

106517

AN:

152002

Hom.:

37619

Cov.:

AF XY:

0.702

AC XY:

52166

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.731

Gnomad4 AMR

AF:

0.701

Gnomad4 ASJ

AF:

0.692

Gnomad4 EAS

AF:

0.900

Gnomad4 SAS

AF:

0.775

Gnomad4 FIN

AF:

0.609

Gnomad4 NFE

AF:

0.677

Gnomad4 OTH

AF:

0.675

Alfa

AF:

0.691

Hom.:

7530

Bravo

AF:

0.707

Asia WGS

AF:

0.847

AC:

2944

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 27, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

7.2

DANN

Benign

0.62

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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