14-65615855-A-G

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.204-123A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 638,516 control chromosomes in the GnomAD database, including 62,171 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.35 (11922 hom., cov: 33)
  • Exomes 𝑓: 0.44 (50249 hom.)
• Consequence: FUT8 NM_001371533.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.848

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 14-65615855-A-G is Benign according to our data. Variant chr14-65615855-A-G is described in ClinVar as [Benign]. Clinvar id is 1236941.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FUT8	NM_001371533.1	c.204-123A>G		intron_variant		ENST00000673929.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FUT8	ENST00000673929.1	c.204-123A>G		intron_variant			NM_001371533.1	P1

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53914 AN: 152042 Hom.: 11913 Cov.: 33

Gnomad AFR AF: 0.0972

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.352

GnomAD4 exome AF: 0.439 AC: 213416 AN: 486354 Hom.: 50249 AF XY: 0.436 AC XY: 111075 AN XY: 254858

Gnomad4 AFR exome AF: 0.0951

Gnomad4 AMR exome AF: 0.384

Gnomad4 ASJ exome AF: 0.443

Gnomad4 EAS exome AF: 0.154

Gnomad4 SAS exome AF: 0.335

Gnomad4 FIN exome AF: 0.463

Gnomad4 NFE exome AF: 0.499

Gnomad4 OTH exome AF: 0.429

GnomAD4 genome AF: 0.354 AC: 53920 AN: 152162 Hom.: 11922 Cov.: 33 AF XY: 0.353 AC XY: 26234 AN XY: 74380

Gnomad4 AFR AF: 0.0969

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.347

Alfa AF: 0.428 Hom.: 2465

Bravo AF: 0.339

Asia WGS AF: 0.247 AC: 856 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

Jul 27, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	7.0
Dann	Benign	0.74

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: rs8012278; hg19: chr14-66082573; COSMIC: COSV61281754;