chr6-96108727-G-A

Variant names:

• chr6-96108727-G-A
• rs7768089
• NM_006581.4:c.-97-5312G>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.-97-5312G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,852 control chromosomes in the GnomAD database, including 13,720 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 0.42 (13720 hom., cov: 32)
• Consequence: FUT9 NM_006581.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 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.-97-5312G>A		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.-97-5312G>A		intron	N/A	ENSP00000302599.4	Q9Y231
	FUT9	ENST00000887181.1		c.-97-5312G>A		intron	N/A	ENSP00000557240.1
	FUT9	ENST00000887182.1		c.-97-5312G>A		intron	N/A	ENSP00000557241.1

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63562 AN: 151734 Hom.: 13716 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.419 AC: 63605 AN: 151852 Hom.: 13720 Cov.: 32 AF XY: 0.426 AC XY: 31594 AN XY: 74204

African (AFR) AF: 0.384 AC: 15902 AN: 41412

American (AMR) AF: 0.513 AC: 7820 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1202 AN: 3468

East Asian (EAS) AF: 0.608 AC: 3124 AN: 5142

South Asian (SAS) AF: 0.583 AC: 2804 AN: 4810

European-Finnish (FIN) AF: 0.429 AC: 4517 AN: 10522

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26862 AN: 67932

Other (OTH) AF: 0.440 AC: 930 AN: 2112

Alfa AF: 0.403 Hom.: 36254

Bravo AF: 0.420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.16
DANN	Benign	0.38
PhyloP100		-2.0
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: rs7768089; hg19: chr6-96556603; COSMIC: COSV56155350;