Genetic Variant FUT9:c.*8003G>A (chr6-96212238-G-A) – 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.*8003G>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 0.139 in 412,524 control chromosomes in the GnomAD database, including 4,737 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 0.12 ( 1468 hom., cov: 32)

Exomes 𝑓: 0.15 ( 3269 hom. )

Consequence

FUT9
NM_006581.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.216

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:

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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=-0.77).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FUT9	NM_006581.4 link	c.*8003G>A		3_prime_UTR_variant	Exon 3 of 3	ENST00000302103.6	NP_006572.2	Q9Y231

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
FUT9	ENST00000302103.6 link	c.*8003G>A	3_prime_UTR_variant	Exon 3 of 3	1	NM_006581.4	ENSP00000302599.4	Q9Y231
UFL1-AS1	ENST00000658843.2 link	n.302-9223C>T	intron_variant	Intron 3 of 3
UFL1-AS1	ENST00000662501.1 link	n.394-9223C>T	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18767

AN:

151760

Hom.:

1468

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0624

Gnomad AMI

AF:

0.266

Gnomad AMR

AF:

0.0911

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0503

Gnomad FIN

AF:

0.124

Gnomad MID

AF:

0.0669

Gnomad NFE

AF:

0.181

Gnomad OTH

AF:

0.123

GnomAD4 exome

AF:

0.147

AC:

38436

AN:

260646

Hom.:

3269

Cov.:

AF XY:

0.151

AC XY:

19875

AN XY:

131596

show subpopulations

Gnomad4 AFR exome

AF:

0.0664

AC:

476

AN:

7166

Gnomad4 AMR exome

AF:

0.0952

AC:

708

AN:

7434

Gnomad4 ASJ exome

AF:

0.135

AC:

1241

AN:

9224

Gnomad4 EAS exome

AF:

0.000262

AC:

AN:

22874

Gnomad4 SAS exome

AF:

0.0397

AC:

120

AN:

3026

Gnomad4 FIN exome

AF:

0.126

AC:

4471

AN:

35480

Gnomad4 NFE exome

AF:

0.184

AC:

29081

AN:

157710

Gnomad4 Remaining exome

AF:

0.135

AC:

2211

AN:

16438

Heterozygous variant carriers

2028

4056

6083

8111

10139

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

112

224

336

448

560

<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:

0.124

AC:

18767

AN:

151878

Hom.:

1468

Cov.:

AF XY:

0.120

AC XY:

8893

AN XY:

74240

show subpopulations

Gnomad4 AFR

AF:

0.0624

AC:

0.0624096

AN:

0.0624096

Gnomad4 AMR

AF:

0.0910

AC:

0.0910226

AN:

0.0910226

Gnomad4 ASJ

AF:

0.134

AC:

0.133795

AN:

0.133795

Gnomad4 EAS

AF:

0.00116

AC:

0.00116099

AN:

0.00116099

Gnomad4 SAS

AF:

0.0493

AC:

0.0493367

AN:

0.0493367

Gnomad4 FIN

AF:

0.124

AC:

0.123864

AN:

0.123864

Gnomad4 NFE

AF:

0.181

AC:

0.180731

AN:

0.180731

Gnomad4 OTH

AF:

0.121

AC:

0.120837

AN:

0.120837

Heterozygous variant carriers

830

1661

2491

3322

4152

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

210

420

630

840

1050

<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:

0.151

Hom.:

1217

Bravo

AF:

0.121

Asia WGS

AF:

0.0300

AC:

108

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

4.3

DANN

Benign

0.58

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over