rs4380761

Variant names:

• chr6-96157757-A-G
• rs4380761
• NM_006581.4:c.-9+43630A>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+43630A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,984 control chromosomes in the GnomAD database, including 13,755 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 0.41 (13755 hom., cov: 32)
• Consequence: FUT9 NM_006581.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FUT9	NM_006581.4	c.-9+43630A>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+43630A>G		intron_variant	Intron 2 of 2	1	NM_006581.4	ENSP00000302599.4

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61765 AN: 151866 Hom.: 13772 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.406 AC: 61750 AN: 151984 Hom.: 13755 Cov.: 32 AF XY: 0.410 AC XY: 30460 AN XY: 74280

African (AFR) AF: 0.240 AC: 9972 AN: 41516

American (AMR) AF: 0.397 AC: 6068 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2051 AN: 3466

East Asian (EAS) AF: 0.600 AC: 3090 AN: 5154

South Asian (SAS) AF: 0.703 AC: 3388 AN: 4820

European-Finnish (FIN) AF: 0.422 AC: 4449 AN: 10544

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31179 AN: 67892

Other (OTH) AF: 0.437 AC: 922 AN: 2112

Alfa AF: 0.456 Hom.: 8654

Bravo AF: 0.393

Asia WGS AF: 0.650 AC: 2249 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.8
DANN	Benign	0.87
PhyloP100		0.27
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: rs4380761; hg19: chr6-96605633; COSMIC: COSV56151297;