19-5839735-G-A

Variant names:

• chr19-5839735-G-A
• rs3760776
• NM_000150.4:c.-1199C>T

Variant summary

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

The NM_000150.4(FUT6):​c.-1199C>T 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
• Publications: 40 publications found

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]

FUT6 Gene-Disease associations (from GenCC):

• fucosyltransferase 6 deficiency

  Inheritance: AR Classification: NO_KNOWN Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000150.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FUT6	NM_000150.4	MANE Select	c.-1199C>T		upstream_gene	N/A	NP_000141.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FUT6	ENST00000318336.10	TSL:2 MANE Select	c.-1199C>T		upstream_gene	N/A	ENSP00000313398.4
	FUT6	ENST00000286955.5	TSL:1	c.-1071C>T		upstream_gene	N/A	ENSP00000286955.5
	FUT6	ENST00000524754.1	TSL:5	c.-683C>T		upstream_gene	N/A	ENSP00000431708.1

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

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.125 AC: 1 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.125 AC: 1 AN: 8

Other (OTH) AF: 0.500 AC: 2 AN: 4

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

African (AFR) AF: 0.481 AC: 19925 AN: 41420

American (AMR) AF: 0.125 AC: 1904 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 610 AN: 3472

East Asian (EAS) AF: 0.163 AC: 841 AN: 5174

South Asian (SAS) AF: 0.191 AC: 920 AN: 4820

European-Finnish (FIN) AF: 0.0932 AC: 988 AN: 10600

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.0945 AC: 6425 AN: 67994

Other (OTH) AF: 0.196 AC: 414 AN: 2110

Alfa AF: 0.125 Hom.: 7933

Bravo AF: 0.222

Asia WGS AF: 0.241 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.82
DANN	Benign	0.33
PhyloP100		-0.15
PromoterAI		-0.0078	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3760776; hg19: chr19-5839746;