rs4440473

Variant names:

• chr6-96204830-G-A
• rs4440473
• NM_006581.4:c.*595G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-96204830-G-A
• chr6-96204830-G-C
• chr6-96204830-G-T

Variant summary

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

The NM_006581.4(FUT9):​c.*595G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.92 in 166,380 control chromosomes in the GnomAD database, including 71,822 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 (64691 hom., cov: 32)
  • Exomes 𝑓: 1.0 (7131 hom.)
• Consequence: FUT9 NM_006581.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• 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]

UFL1-AS1 (HGNC:41007): (UFL1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 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.*595G>A		3_prime_UTR	Exon 3 of 3	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.*595G>A		3_prime_UTR	Exon 3 of 3	ENSP00000302599.4	Q9Y231
	FUT9	ENST00000887181.1		c.*595G>A		3_prime_UTR	Exon 4 of 4	ENSP00000557240.1
	FUT9	ENST00000887182.1		c.*595G>A		3_prime_UTR	Exon 4 of 4	ENSP00000557241.1

Frequencies

GnomAD3 genomes AF: 0.913 AC: 138737 AN: 151990 Hom.: 64656 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.969

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.977

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.930

GnomAD4 exome AF: 1.00 AC: 14266 AN: 14272 Hom.: 7131 Cov.: 0 AF XY: 0.999 AC XY: 6770 AN XY: 6774

African (AFR) AF: 0.750 AC: 3 AN: 4

American (AMR) AF: 1.00 AC: 4 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 4 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 14085 AN: 14088

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.976 AC: 82 AN: 84

Other (OTH) AF: 1.00 AC: 86 AN: 86

GnomAD4 genome AF: 0.913 AC: 138823 AN: 152108 Hom.: 64691 Cov.: 32 AF XY: 0.916 AC XY: 68099 AN XY: 74370

African (AFR) AF: 0.701 AC: 29072 AN: 41446

American (AMR) AF: 0.969 AC: 14790 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.997 AC: 3462 AN: 3472

East Asian (EAS) AF: 0.992 AC: 5144 AN: 5186

South Asian (SAS) AF: 0.978 AC: 4718 AN: 4826

European-Finnish (FIN) AF: 1.00 AC: 10617 AN: 10620

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67851 AN: 67978

Other (OTH) AF: 0.931 AC: 1968 AN: 2114

Alfa AF: 0.931 Hom.: 27621

Bravo AF: 0.901

Asia WGS AF: 0.973 AC: 3374 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.072
DANN	Benign	0.36
PhyloP100		-0.21
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: rs4440473; hg19: chr6-96652706;