6-96147920-T-G

Variant names:

• chr6-96147920-T-G
• rs4361623
• NM_006581.4:c.-9+33793T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006581.4(FUT9):​c.-9+33793T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.914 in 150,956 control chromosomes in the GnomAD database, including 64,327 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 0.91 (64327 hom., cov: 26)
• Consequence: FUT9 NM_006581.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.867
• Publications: 0 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FUT9	NM_006581.4	c.-9+33793T>G		intron_variant	Intron 2 of 2	ENST00000302103.6	NP_006572.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FUT9	ENST00000302103.6	c.-9+33793T>G		intron_variant	Intron 2 of 2	1	NM_006581.4	ENSP00000302599.4

Frequencies

GnomAD3 genomes AF: 0.914 AC: 137858 AN: 150840 Hom.: 64291 Cov.: 26

Gnomad AFR AF: 0.703

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.979

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.933

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

GnomAD4 genome AF: 0.914 AC: 137946 AN: 150956 Hom.: 64327 Cov.: 26 AF XY: 0.917 AC XY: 67541 AN XY: 73664

African (AFR) AF: 0.703 AC: 28740 AN: 40876

American (AMR) AF: 0.970 AC: 14617 AN: 15066

Ashkenazi Jewish (ASJ) AF: 0.997 AC: 3460 AN: 3470

East Asian (EAS) AF: 0.992 AC: 5122 AN: 5164

South Asian (SAS) AF: 0.980 AC: 4628 AN: 4724

European-Finnish (FIN) AF: 1.00 AC: 10453 AN: 10456

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67779 AN: 67910

Other (OTH) AF: 0.933 AC: 1947 AN: 2086

Alfa AF: 0.938 Hom.: 8311

Bravo AF: 0.902

Asia WGS AF: 0.974 AC: 3386 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.40
PhyloP100		-0.87
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: rs4361623; hg19: chr6-96595796;