19-5836953-G-A

Variant names:

• chr19-5836953-G-A
• rs1678849
• NM_000150.4:c.-141+1724C>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.-141+1724C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,122 control chromosomes in the GnomAD database, including 41,044 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 0.73 (41044 hom., cov: 32)
• Consequence: FUT6 NM_000150.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.04
• Publications: 5 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 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.-141+1724C>T		intron	N/A	NP_000141.1
	FUT6	NM_001040701.2		c.-13+1724C>T		intron	N/A	NP_001035791.1
	FUT6	NM_001369502.1		c.-186+1724C>T		intron	N/A	NP_001356431.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FUT6	ENST00000318336.10	TSL:2 MANE Select	c.-141+1724C>T		intron	N/A	ENSP00000313398.4
	FUT6	ENST00000286955.5	TSL:1	c.-13+1724C>T		intron	N/A	ENSP00000286955.5
	FUT6	ENST00000527106.5	TSL:1	c.-186+1724C>T		intron	N/A	ENSP00000432954.1

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111282 AN: 152004 Hom.: 40990 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.732 AC: 111396 AN: 152122 Hom.: 41044 Cov.: 32 AF XY: 0.734 AC XY: 54600 AN XY: 74348

African (AFR) AF: 0.762 AC: 31616 AN: 41506

American (AMR) AF: 0.793 AC: 12110 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2437 AN: 3472

East Asian (EAS) AF: 0.866 AC: 4490 AN: 5184

South Asian (SAS) AF: 0.651 AC: 3136 AN: 4816

European-Finnish (FIN) AF: 0.740 AC: 7823 AN: 10570

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47407 AN: 67986

Other (OTH) AF: 0.740 AC: 1563 AN: 2112

Alfa AF: 0.712 Hom.: 111921

Bravo AF: 0.739

Asia WGS AF: 0.795 AC: 2764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.45
DANN	Benign	0.36
PhyloP100		-4.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1678849; hg19: chr19-5836964;