NM_006581.4:c.*595G>A

Variant summary

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

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.211

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

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=-1.02).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FUT9NM_006581.4 linkc.*595G>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
FUT9ENST00000302103.6 linkc.*595G>A 3_prime_UTR_variant Exon 3 of 3 1 NM_006581.4 ENSP00000302599.4 Q9Y231

Frequencies

GnomAD3 genomes
AF:
0.913
AC:
138737
AN:
151990
Hom.:
64656
Cov.:
32
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:
14266
AN:
14272
Hom.:
7131
Cov.:
0
AF XY:
0.999
AC XY:
6770
AN XY:
6774
show subpopulations
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
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.488
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.913
AC:
138823
AN:
152108
Hom.:
64691
Cov.:
32
AF XY:
0.916
AC XY:
68099
AN XY:
74370
show subpopulations
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
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
484
967
1451
1934
2418
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
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:
0.931
Hom.:
27621
Bravo
AF:
0.901
Asia WGS
AF:
0.973
AC:
3374
AN:
3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

Other links and lift over

dbSNP: rs4440473; hg19: chr6-96652706; API