rs7147624

Variant names:

• chr14-65398907-T-G
• rs7147624
• XM_047431179.1:c.-390+22033T>G

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

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: DEFINITIVE, STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P, ClinGen

ENSG00000300981 (HGNC:):

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775339.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300981	ENST00000775339.1		n.121+14683A>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7147624;

hg19: chr14-65865625;