chr6-96204830-G-A
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Variant summary
Our verdict is Benign. Variant got -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
NM_006581.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.211
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FUT9 | NM_006581.4 | c.*595G>A | 3_prime_UTR_variant | 3/3 | ENST00000302103.6 | ||
UFL1-AS1 | XR_007059687.1 | n.9276-1815C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FUT9 | ENST00000302103.6 | c.*595G>A | 3_prime_UTR_variant | 3/3 | 1 | NM_006581.4 | P1 | ||
UFL1-AS1 | ENST00000658843.2 | n.302-1815C>T | intron_variant, non_coding_transcript_variant | ||||||
UFL1-AS1 | ENST00000662501.1 | n.394-1815C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.913 AC: 138737AN: 151990Hom.: 64656 Cov.: 32
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GnomAD4 exome AF: 1.00 AC: 14266AN: 14272Hom.: 7131 Cov.: 0 AF XY: 0.999 AC XY: 6770AN XY: 6774
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GnomAD4 genome AF: 0.913 AC: 138823AN: 152108Hom.: 64691 Cov.: 32 AF XY: 0.916 AC XY: 68099AN XY: 74370
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at