dbSNP rs7745248: 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

Publications

8 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=-0.77).

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	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FUT9	ENST00000302103.6 link	c.*8003G>A		3_prime_UTR_variant	Exon 3 of 3	1	NM_006581.4	ENSP00000302599.4		Q9Y231

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

African (AFR)

AF:

0.0664

AC:

476

AN:

7166

American (AMR)

AF:

0.0952

AC:

708

AN:

7434

Ashkenazi Jewish (ASJ)

AF:

0.135

AC:

1241

AN:

9224

East Asian (EAS)

AF:

0.000262

AC:

AN:

22874

South Asian (SAS)

AF:

0.0397

AC:

120

AN:

3026

European-Finnish (FIN)

AF:

0.126

AC:

4471

AN:

35480

Middle Eastern (MID)

AF:

0.0943

AC:

122

AN:

1294

European-Non Finnish (NFE)

AF:

0.184

AC:

29081

AN:

157710

Other (OTH)

AF:

0.135

AC:

2211

AN:

16438

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

2028

4056

6083

8111

10139

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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

African (AFR)

AF:

0.0624

AC:

2590

AN:

41500

American (AMR)

AF:

0.0910

AC:

1385

AN:

15216

Ashkenazi Jewish (ASJ)

AF:

0.134

AC:

464

AN:

3468

East Asian (EAS)

AF:

0.00116

AC:

AN:

5168

South Asian (SAS)

AF:

0.0493

AC:

238

AN:

4824

European-Finnish (FIN)

AF:

0.124

AC:

1309

AN:

10568

Middle Eastern (MID)

AF:

0.0685

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.181

AC:

12259

AN:

67830

Other (OTH)

AF:

0.121

AC:

254

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

830

1661

2491

3322

4152

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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

(source)

DANN

Benign

0.58

PhyloP100

0.22

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over