chr19-5839735-G-A

Position:

• chr19-5839735-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The 19-5839735-G-A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,098 control chromosomes in the GnomAD database, including 5,593 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 0.21 (5591 hom., cov: 31)
  • Exomes 𝑓: 0.27 (2 hom.)
• Consequence: FUT6 NM_000150.4 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150

Genes affected

FUT6 (HGNC:4017): (fucosyltransferase 6) The protein encoded by this gene is a Golgi stack membrane protein that is involved in the creation of sialyl-Lewis X, an E-selectin ligand. Mutations in this gene are a cause of fucosyltransferase-6 deficiency. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FUT6	NM_000150.4			upstream_gene_variant		ENST00000318336.10	NP_000141.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FUT6	ENST00000318336.10			upstream_gene_variant		2	NM_000150.4	ENSP00000313398	P1
FUT6	ENST00000286955.5			upstream_gene_variant		1		ENSP00000286955	P1
FUT6	ENST00000524754.1			upstream_gene_variant		5		ENSP00000431708	P1
FUT6	ENST00000591079.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32049 AN: 151958 Hom.: 5572 Cov.: 31

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.0932

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0945

Gnomad OTH AF: 0.193

GnomAD4 exome AF: 0.273 AC: 6 AN: 22 Hom.: 2 Cov.: 0 AF XY: 0.0833 AC XY: 1 AN XY: 12

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.125

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.211 AC: 32114 AN: 152076 Hom.: 5591 Cov.: 31 AF XY: 0.210 AC XY: 15610 AN XY: 74330

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.0932

Gnomad4 NFE AF: 0.0945

Gnomad4 OTH AF: 0.196

Alfa AF: 0.114 Hom.: 3091

Bravo AF: 0.222

Asia WGS AF: 0.241 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.82
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3760776; hg19: chr19-5839746;