dbSNP rs3760776: FUT6:c.-1199C>T (chr19-5839735-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_000150.4(FUT6):c.-1199C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,098 control chromosomes in the GnomAD database, including 5,593 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 0.21 ( 5591 hom., cov: 31)

Exomes 𝑓: 0.27 ( 2 hom. )

Consequence

FUT6
NM_000150.4 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.150

Publications

40 publications found

Variant links:

Genes affected

FUT6 (HGNC:4017): (fucosyltransferase 6) The protein encoded by this gene is a Golgi stack membrane protein that is involved in the creation of sialyl-Lewis X, an E-selectin ligand. Mutations in this gene are a cause of fucosyltransferase-6 deficiency. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

FUT6 Gene-Disease associations (from GenCC):

fucosyltransferase 6 deficiency
Inheritance: AR Classification: NO_KNOWN Submitted by: Ambry Genetics

FUT6 links:

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FUT6	NM_000150.4 link	c.-1199C>T		upstream_gene_variant		ENST00000318336.10	NP_000141.1	P51993-1Q6P7E6

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
FUT6	ENST00000318336.10 link	c.-1199C>T	upstream_gene_variant	2	NM_000150.4	ENSP00000313398.4	P51993-1
FUT6	ENST00000286955.5 link	c.-1071C>T	upstream_gene_variant	1		ENSP00000286955.5	P51993-1
FUT6	ENST00000524754.1 link	c.-683C>T	upstream_gene_variant	5		ENSP00000431708.1	P51993-1
FUT6	ENST00000591079.1 link	n.-13C>T	upstream_gene_variant	6

Frequencies

GnomAD3 genomes

AF:

0.211

AC:

32049

AN:

151958

Hom.:

5572

Cov.:

show subpopulations

Gnomad AFR

AF:

0.481

Gnomad AMI

AF:

0.0329

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.176

Gnomad EAS

AF:

0.163

Gnomad SAS

AF:

0.191

Gnomad FIN

AF:

0.0932

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.0945

Gnomad OTH

AF:

0.193

GnomAD4 exome

AF:

0.273

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0833

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.125

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.125

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.400

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.211

AC:

32114

AN:

152076

Hom.:

5591

Cov.:

AF XY:

0.210

AC XY:

15610

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.481

AC:

19925

AN:

41420

American (AMR)

AF:

0.125

AC:

1904

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.176

AC:

610

AN:

3472

East Asian (EAS)

AF:

0.163

AC:

841

AN:

5174

South Asian (SAS)

AF:

0.191

AC:

920

AN:

4820

European-Finnish (FIN)

AF:

0.0932

AC:

988

AN:

10600

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0945

AC:

6425

AN:

67994

Other (OTH)

AF:

0.196

AC:

414

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1078

2157

3235

4314

5392

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

302

604

906

1208

1510

<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:

0.125

Hom.:

7933

Bravo

AF:

0.222

Asia WGS

AF:

0.241

AC:

838

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.82

(source)

DANN

Benign

0.33

PhyloP100

-0.15

PromoterAI

-0.0078

Neutral

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over