Genetic Variant FUT9:c.*471G>T (chr6-96204706-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006581.4(FUT9):c.*471G>T 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 167,000 control chromosomes in the GnomAD database, including 72,117 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 ( 64714 hom., cov: 32)

Exomes 𝑓: 1.0 ( 7403 hom. )

Consequence

FUT9
NM_006581.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.30

Publications

1 publications found

Variant links:

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]

FUT9 links:

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

UFL1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.04).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FUT9	NM_006581.4	MANE Select	c.*471G>T		3_prime_UTR	Exon 3 of 3	NP_006572.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FUT9	ENST00000302103.6	TSL:1 MANE Select	c.*471G>T	3_prime_UTR	Exon 3 of 3	ENSP00000302599.4
UFL1-AS1	ENST00000658843.2		n.302-1691C>A	intron	N/A
UFL1-AS1	ENST00000662501.1		n.394-1691C>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.913

AC:

138784

AN:

152062

Hom.:

64679

Cov.:

show subpopulations

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:

0.999

AC:

14811

AN:

14820

Hom.:

7403

Cov.:

AF XY:

0.999

AC XY:

7045

AN XY:

7050

show subpopulations

African (AFR)

AF:

0.667

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

14567

AN:

14570

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.985

AC:

128

AN:

130

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.415

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.913

AC:

138870

AN:

152180

Hom.:

64714

Cov.:

AF XY:

0.916

AC XY:

68142

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.701

AC:

29085

AN:

41482

American (AMR)

AF:

0.969

AC:

14806

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.997

AC:

3462

AN:

3472

East Asian (EAS)

AF:

0.992

AC:

5130

AN:

5172

South Asian (SAS)

AF:

0.978

AC:

4724

AN:

4832

European-Finnish (FIN)

AF:

1.00

AC:

10615

AN:

10618

Middle Eastern (MID)

AF:

0.983

AC:

289

AN:

294

European-Non Finnish (NFE)

AF:

0.998

AC:

67877

AN:

68004

Other (OTH)

AF:

0.931

AC:

1970

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

482

965

1447

1930

2412

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

896

1792

2688

3584

4480

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.941

Hom.:

99786

Bravo

AF:

0.901

Asia WGS

AF:

0.974

AC:

3379

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.039

(source)

DANN

Benign

0.42

PhyloP100

-2.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over