rs1678849

Positions:

• chr19-5836953-G-A
• chr19-5836953-G-C
• chr19-5836953-G-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FUT6	NM_000150.4	c.-141+1724C>T		intron_variant		ENST00000318336.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FUT6	ENST00000318336.10	c.-141+1724C>T		intron_variant		2	NM_000150.4	P1

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

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.793

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.740

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.740

Alfa AF: 0.707 Hom.: 50030

Bravo AF: 0.739

Asia WGS AF: 0.795 AC: 2764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.45
DANN	Benign	0.36

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: rs1678849; hg19: chr19-5836964;