rs10499003

Positions:

• chr6-96057343-A-C
• chr6-96057343-A-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+41131A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,224 control chromosomes in the GnomAD database, including 1,314 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 0.12 (1314 hom., cov: 32)
• Consequence: FUT9 NM_006581.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

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]

LOC105377905 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FUT9	NM_006581.4	c.-98+41131A>C		intron_variant		ENST00000302103.6
LOC105377905	XR_007059689.1	n.5528T>G		non_coding_transcript_exon_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FUT9	ENST00000302103.6	c.-98+41131A>C		intron_variant		1	NM_006581.4	P1

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17644 AN: 152106 Hom.: 1314 Cov.: 32

Gnomad AFR AF: 0.0608

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.0832

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0490

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.116 AC: 17641 AN: 152224 Hom.: 1314 Cov.: 32 AF XY: 0.112 AC XY: 8361 AN XY: 74424

Gnomad4 AFR AF: 0.0608

Gnomad4 AMR AF: 0.0831

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0481

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.118

Alfa AF: 0.147 Hom.: 2485

Bravo AF: 0.113

Asia WGS AF: 0.0280 AC: 100 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.75

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: rs10499003; hg19: chr6-96505219;