14-65561787-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0890

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]

ACMG classification

Verdict is Benign. Variant got -14 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_single_submitter, 1 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	UniProt
FUT8	NM_001371533.1	c.203+21T>C		intron_variant		ENST00000673929.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FUT8	ENST00000673929.1	c.203+21T>C		intron_variant			NM_001371533.1	P1

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106416 AN: 151884 Hom.: 37575 Cov.: 32

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

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.: 24 AF XY: 0.695 AC XY: 494892 AN XY: 712242

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.: 32 AF XY: 0.702 AC XY: 52166 AN XY: 74300

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:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

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

Other links and lift over

dbSNP: rs3825639; hg19: chr14-66028505;