rs7147624

Variant names:

• chr14-65398907-T-G
• rs7147624
• ENST00000775339.1:n.121+14683A>C

Variant summary

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

The ENST00000775339.1(ENSG00000300981):​n.121+14683A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,190 control chromosomes in the GnomAD database, including 51,682 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 0.82 (51682 hom., cov: 32)
• Consequence: ENSG00000300981 ENST00000775339.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 8 publications found

Genes affected

ENSG00000300981 (HGNC:):

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FUT8	XM_047431179.1	c.-390+22033T>G		intron_variant	Intron 3 of 14		XP_047287135.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300981	ENST00000775339.1	n.121+14683A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124939 AN: 152072 Hom.: 51643 Cov.: 32

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.822 AC: 125037 AN: 152190 Hom.: 51682 Cov.: 32 AF XY: 0.826 AC XY: 61498 AN XY: 74422

African (AFR) AF: 0.741 AC: 30733 AN: 41494

American (AMR) AF: 0.812 AC: 12417 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 3080 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5179 AN: 5194

South Asian (SAS) AF: 0.891 AC: 4295 AN: 4818

European-Finnish (FIN) AF: 0.870 AC: 9218 AN: 10594

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57379 AN: 68012

Other (OTH) AF: 0.824 AC: 1742 AN: 2114

Alfa AF: 0.839 Hom.: 40962

Bravo AF: 0.813

Asia WGS AF: 0.934 AC: 3246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.56
PhyloP100		-0.24

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7147624; hg19: chr14-65865625;