NM_006581.4:c.*6324C>T

Variant names:

• chr6-96210559-C-T
• rs4621639
• NM_006581.4:c.*6324C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353
• Publications: 1 publications found

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)

ACMG classification

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FUT9	NM_006581.4	c.*6324C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000302103.6	NP_006572.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FUT9	ENST00000302103.6	c.*6324C>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_006581.4	ENSP00000302599.4

Frequencies

GnomAD3 genomes AF: 0.913 AC: 138601 AN: 151848 Hom.: 64594 Cov.: 31

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.: 0 AF XY: 0.999 AC XY: 7032 AN XY: 7036

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: 14649 AN: 14652

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.976 AC: 80 AN: 82

Other (OTH) AF: 1.00 AC: 90 AN: 90

GnomAD4 genome AF: 0.913 AC: 138687 AN: 151966 Hom.: 64629 Cov.: 31 AF XY: 0.916 AC XY: 68029 AN XY: 74290

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

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.39
DANN	Benign	0.44
PhyloP100		-0.35
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

Other links and lift over

dbSNP: rs4621639; hg19: chr6-96658435;