rs4002794

Positions:

• chr6-96064069-C-G
• chr6-96064069-C-T

Variant summary

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

The NM_006581.4(FUT9):​c.-98+47857C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,846 control chromosomes in the GnomAD database, including 23,587 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 0.56 (23587 hom., cov: 31)
• Consequence: FUT9 NM_006581.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

FUT9 (HGNC:4020): (fucosyltransferase 9) The protein encoded by this gene belongs to the glycosyltransferase family. It is localized to the golgi, and catalyzes the last step in the biosynthesis of Lewis X (LeX) antigen, the addition of a fucose to precursor polysaccharides. This protein is one of the few fucosyltransferases that synthesizes the LeX oligosaccharide (CD15) expressed in the organ buds progressing in mesenchyma during embryogenesis. It is also responsible for the expression of CD15 in mature granulocytes. A common haplotype of this gene has also been associated with susceptibility to placental malaria infection. [provided by RefSeq, Nov 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FUT9	NM_006581.4	c.-98+47857C>G		intron_variant		ENST00000302103.6	NP_006572.2
FUT9	XM_017010190.2	c.-215+47857C>G		intron_variant			XP_016865679.1
FUT9	XM_047418088.1	c.-98+43096C>G		intron_variant			XP_047274044.1
FUT9	XM_047418089.1	c.-215+43096C>G		intron_variant			XP_047274045.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FUT9	ENST00000302103.6	c.-98+47857C>G		intron_variant		1	NM_006581.4	ENSP00000302599.4

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84406 AN: 151728 Hom.: 23575 Cov.: 31

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.556 AC: 84463 AN: 151846 Hom.: 23587 Cov.: 31 AF XY: 0.560 AC XY: 41512 AN XY: 74186

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.580

Alfa AF: 0.563 Hom.: 2992

Bravo AF: 0.558

Asia WGS AF: 0.633 AC: 2201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.066
DANN	Benign	0.39

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: rs4002794; hg19: chr6-96511945;