14-65615775-C-T

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.204-203C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,142 control chromosomes in the GnomAD database, including 1,726 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.13 (1726 hom., cov: 32)
• Consequence: FUT8 NM_001371533.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.252

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=-0.82).
• BP6: Variant 14-65615775-C-T is Benign according to our data. Variant chr14-65615775-C-T is described in ClinVar as [Benign]. Clinvar id is 1289341.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FUT8	NM_001371533.1	c.204-203C>T		intron_variant		ENST00000673929.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FUT8	ENST00000673929.1	c.204-203C>T		intron_variant			NM_001371533.1	P1

Frequencies

GnomAD3 genomes AF: 0.132 AC: 19993 AN: 152022 Hom.: 1723 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.0720

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0813

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.132 AC: 20024 AN: 152142 Hom.: 1726 Cov.: 32 AF XY: 0.134 AC XY: 9986 AN XY: 74370

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.0720

Gnomad4 NFE AF: 0.0813

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0464 Hom.: 35

Bravo AF: 0.139

Asia WGS AF: 0.248 AC: 861 AN: 3474

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

Oct 16, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	9.6
Dann	Benign	0.65

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: rs2073294; hg19: chr14-66082493;