6-96204706-G-T

Position:

• chr6-96204706-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006581.4(FUT9):​c.*471G>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 167,000 control chromosomes in the GnomAD database, including 72,117 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 (64714 hom., cov: 32)
  • Exomes 𝑓: 1.0 (7403 hom.)
• Consequence: FUT9 NM_006581.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• 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	Protein	UniProt
FUT9	NM_006581.4	c.*471G>T		3_prime_UTR_variant	3/3	ENST00000302103.6	NP_006572.2
UFL1-AS1	XR_007059687.1	n.9276-1691C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FUT9	ENST00000302103.6	c.*471G>T		3_prime_UTR_variant	3/3	1	NM_006581.4	ENSP00000302599	P1
UFL1-AS1	ENST00000658843.2	n.302-1691C>A		intron_variant, non_coding_transcript_variant
UFL1-AS1	ENST00000662501.1	n.394-1691C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.913 AC: 138784 AN: 152062 Hom.: 64679 Cov.: 32

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: 0.999 AC: 14811 AN: 14820 Hom.: 7403 Cov.: 0 AF XY: 0.999 AC XY: 7045 AN XY: 7050

Gnomad4 AFR exome AF: 0.667

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.985

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.913 AC: 138870 AN: 152180 Hom.: 64714 Cov.: 32 AF XY: 0.916 AC XY: 68142 AN XY: 74420

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.969

Gnomad4 ASJ AF: 0.997

Gnomad4 EAS AF: 0.992

Gnomad4 SAS AF: 0.978

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.998

Gnomad4 OTH AF: 0.931

Alfa AF: 0.971 Hom.: 68252

Bravo AF: 0.901

Asia WGS AF: 0.974 AC: 3379 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.039
DANN	Benign	0.42

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

Other links and lift over

dbSNP: rs4454149; hg19: chr6-96652582;