6-96111973-C-T

Position:

• chr6-96111973-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006581.4(FUT9):​c.-97-2066C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,958 control chromosomes in the GnomAD database, including 13,868 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 (13868 hom., cov: 32)
• Consequence: FUT9 NM_006581.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FUT9	NM_006581.4	c.-97-2066C>T		intron_variant		ENST00000302103.6	NP_006572.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FUT9	ENST00000302103.6	c.-97-2066C>T		intron_variant		1	NM_006581.4	ENSP00000302599.4

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63938 AN: 151842 Hom.: 13867 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.421 AC: 63979 AN: 151958 Hom.: 13868 Cov.: 32 AF XY: 0.428 AC XY: 31777 AN XY: 74268

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.442

Alfa AF: 0.407 Hom.: 1569

Bravo AF: 0.422

Asia WGS AF: 0.598 AC: 2078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	4.1
DANN	Benign	0.84

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: rs3811070; hg19: chr6-96559849; COSMIC: COSV56155360;