Genetic Variant FUT9:c.*6324C>T (chr6-96210559-C-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.*6324C>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 166,804 control chromosomes in the GnomAD database, including 72,043 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 ( 64629 hom., cov: 31)

Exomes 𝑓: 1.0 ( 7414 hom. )

Consequence

FUT9
NM_006581.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.353

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=-0.94).

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.*6324C>T		3_prime_UTR	Exon 3 of 3	NP_006572.2	Q9Y231

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FUT9	ENST00000302103.6	TSL:1 MANE Select	c.*6324C>T	3_prime_UTR	Exon 3 of 3	ENSP00000302599.4	Q9Y231
UFL1-AS1	ENST00000658843.2		n.302-7544G>A	intron	N/A
UFL1-AS1	ENST00000662501.1		n.394-7544G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.913

AC:

138601

AN:

151848

Hom.:

64594

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:

1.00

AC:

14832

AN:

14838

Hom.:

7414

Cov.:

AF XY:

0.999

AC XY:

7032

AN XY:

7036

show subpopulations

African (AFR)

AF:

0.750

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

14649

AN:

14652

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.976

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.413

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.913

AC:

138687

AN:

151966

Hom.:

64629

Cov.:

AF XY:

0.916

AC XY:

68029

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.701

AC:

29033

AN:

41400

American (AMR)

AF:

0.969

AC:

14774

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.997

AC:

3462

AN:

3472

East Asian (EAS)

AF:

0.992

AC:

5123

AN:

5166

South Asian (SAS)

AF:

0.978

AC:

4722

AN:

4830

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:

67787

AN:

67914

Other (OTH)

AF:

0.931

AC:

1968

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

479

957

1436

1914

2393

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.:

28780

Bravo

AF:

0.901

Asia WGS

AF:

0.973

AC:

3386

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.39

(source)

DANN

Benign

0.44

PhyloP100

-0.35

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over