6-96212238-G-A

Position:

• chr6-96212238-G-A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216

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=-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/exons	MANE	Protein	UniProt
FUT9	NM_006581.4	c.*8003G>A		3_prime_UTR_variant	3/3	ENST00000302103.6	NP_006572.2
UFL1-AS1	XR_007059687.1	n.9276-9223C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FUT9	ENST00000302103.6	c.*8003G>A		3_prime_UTR_variant	3/3	1	NM_006581.4	ENSP00000302599	P1
UFL1-AS1	ENST00000658843.2	n.302-9223C>T		intron_variant, non_coding_transcript_variant
UFL1-AS1	ENST00000662501.1	n.394-9223C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18767 AN: 151760 Hom.: 1468 Cov.: 32

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.: 0 AF XY: 0.151 AC XY: 19875 AN XY: 131596

Gnomad4 AFR exome AF: 0.0664

Gnomad4 AMR exome AF: 0.0952

Gnomad4 ASJ exome AF: 0.135

Gnomad4 EAS exome AF: 0.000262

Gnomad4 SAS exome AF: 0.0397

Gnomad4 FIN exome AF: 0.126

Gnomad4 NFE exome AF: 0.184

Gnomad4 OTH exome AF: 0.135

GnomAD4 genome AF: 0.124 AC: 18767 AN: 151878 Hom.: 1468 Cov.: 32 AF XY: 0.120 AC XY: 8893 AN XY: 74240

Gnomad4 AFR AF: 0.0624

Gnomad4 AMR AF: 0.0910

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0493

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.121

Alfa AF: 0.153 Hom.: 1067

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
DANN	Benign	0.58

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: rs7745248; hg19: chr6-96660114;