rs10499003

Variant names:

• chr6-96057343-A-C
• rs10499003
• NM_006581.4:c.-98+41131A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-96057343-A-C
• chr6-96057343-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006581.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FUT9	NM_006581.4	MANE Select	c.-98+41131A>C		intron	N/A	NP_006572.2	Q9Y231

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FUT9	ENST00000302103.6	TSL:1 MANE Select	c.-98+41131A>C		intron	N/A	ENSP00000302599.4	Q9Y231
	FUT9	ENST00000887181.1		c.-98+41131A>C		intron	N/A	ENSP00000557240.1
	FUT9	ENST00000887182.1		c.-98+36370A>C		intron	N/A	ENSP00000557241.1

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

African (AFR) AF: 0.0608 AC: 2525 AN: 41542

American (AMR) AF: 0.0831 AC: 1270 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 433 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5182

South Asian (SAS) AF: 0.0481 AC: 232 AN: 4828

European-Finnish (FIN) AF: 0.118 AC: 1250 AN: 10598

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11387 AN: 68000

Other (OTH) AF: 0.118 AC: 250 AN: 2116

Alfa AF: 0.144 Hom.: 2976

Bravo AF: 0.113

Asia WGS AF: 0.0280 AC: 100 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.75
PhyloP100		0.18
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: rs10499003; hg19: chr6-96505219;