rs9323464

Variant names:

• chr14-65704415-G-A
• rs9323464
• NM_001371533.1:c.836-17360G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001371533.1(FUT8):​c.836-17360G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0616 in 151,950 control chromosomes in the GnomAD database, including 525 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.062 (525 hom., cov: 32)
• Consequence: FUT8 NM_001371533.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.965
• Publications: 2 publications found

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)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FUT8	NM_001371533.1	c.836-17360G>A		intron_variant	Intron 7 of 10	ENST00000673929.1	NP_001358462.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FUT8	ENST00000673929.1	c.836-17360G>A		intron_variant	Intron 7 of 10		NM_001371533.1	ENSP00000501213.1

Frequencies

GnomAD3 genomes AF: 0.0616 AC: 9356 AN: 151836 Hom.: 525 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0270

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0343

Gnomad FIN AF: 0.0177

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0224

Gnomad OTH AF: 0.0427

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0616 AC: 9366 AN: 151950 Hom.: 525 Cov.: 32 AF XY: 0.0604 AC XY: 4486 AN XY: 74244

African (AFR) AF: 0.144 AC: 5985 AN: 41474

American (AMR) AF: 0.0269 AC: 411 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0839 AC: 291 AN: 3470

East Asian (EAS) AF: 0.136 AC: 705 AN: 5170

South Asian (SAS) AF: 0.0339 AC: 158 AN: 4664

European-Finnish (FIN) AF: 0.0177 AC: 188 AN: 10592

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 290

European-Non Finnish (NFE) AF: 0.0224 AC: 1526 AN: 67992

Other (OTH) AF: 0.0422 AC: 89 AN: 2108

Alfa AF: 0.0466 Hom.: 45

Bravo AF: 0.0662

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.78
DANN	Benign	0.59
PhyloP100		-0.96
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9323464; hg19: chr14-66171133;