6-96063813-G-A

Variant names:

• chr6-96063813-G-A
• rs716192
• NM_006581.4:c.-98+47601G>A

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+47601G>A 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 151,914 control chromosomes in the GnomAD database, including 23,572 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 (23572 hom., cov: 31)
• Consequence: FUT9 NM_006581.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FUT9	NM_006581.4	c.-98+47601G>A		intron_variant	Intron 1 of 2	ENST00000302103.6	NP_006572.2
FUT9	XM_017010190.2	c.-215+47601G>A		intron_variant	Intron 1 of 3		XP_016865679.1
FUT9	XM_047418088.1	c.-98+42840G>A		intron_variant	Intron 2 of 3		XP_047274044.1
FUT9	XM_047418089.1	c.-215+42840G>A		intron_variant	Intron 2 of 4		XP_047274045.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FUT9	ENST00000302103.6	c.-98+47601G>A		intron_variant	Intron 1 of 2	1	NM_006581.4	ENSP00000302599.4

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84361 AN: 151796 Hom.: 23560 Cov.: 31

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.556 AC: 84418 AN: 151914 Hom.: 23572 Cov.: 31 AF XY: 0.559 AC XY: 41499 AN XY: 74258

African (AFR) AF: 0.514 AC: 21290 AN: 41404

American (AMR) AF: 0.605 AC: 9246 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1699 AN: 3470

East Asian (EAS) AF: 0.602 AC: 3099 AN: 5144

South Asian (SAS) AF: 0.638 AC: 3069 AN: 4814

European-Finnish (FIN) AF: 0.547 AC: 5768 AN: 10552

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.563 AC: 38289 AN: 67950

Other (OTH) AF: 0.579 AC: 1219 AN: 2106

Alfa AF: 0.559 Hom.: 3578

Bravo AF: 0.557

Asia WGS AF: 0.632 AC: 2199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.56
PhyloP100		-1.6
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: rs716192; hg19: chr6-96511689;