Genetic Variant NM_000150.4:c.-13+749G>A (chr19-5834201-C-T) – 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.-13+749G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 152,134 control chromosomes in the GnomAD database, including 15,795 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 0.44 ( 15791 hom., cov: 33)

Exomes 𝑓: 0.28 ( 4 hom. )

Consequence

FUT6
NM_000150.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.389

Publications

18 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000150.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FUT6	NM_000150.4	MANE Select	c.-13+749G>A	intron	N/A	NP_000141.1
FUT6	NM_001040701.2		c.-12-1622G>A	intron	N/A	NP_001035791.1
FUT6	NM_001369502.1		c.-58+749G>A	intron	N/A	NP_001356431.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FUT6	ENST00000318336.10	TSL:2 MANE Select	c.-13+749G>A	intron	N/A	ENSP00000313398.4
FUT6	ENST00000286955.5	TSL:1	c.-12-1622G>A	intron	N/A	ENSP00000286955.5
FUT6	ENST00000527106.5	TSL:1	c.-58+749G>A	intron	N/A	ENSP00000432954.1

Frequencies

GnomAD3 genomes

AF:

0.436

AC:

66231

AN:

151900

Hom.:

15751

Cov.:

show subpopulations

Gnomad AFR

AF:

0.608

Gnomad AMI

AF:

0.240

Gnomad AMR

AF:

0.484

Gnomad ASJ

AF:

0.369

Gnomad EAS

AF:

0.596

Gnomad SAS

AF:

0.384

Gnomad FIN

AF:

0.398

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.324

Gnomad OTH

AF:

0.458

GnomAD4 exome

AF:

0.284

AC:

AN:

116

Hom.:

AF XY:

0.243

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.304

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.286

AC:

AN:

Other (OTH)

AF:

0.100

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.535

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:

0.436

AC:

66329

AN:

152018

Hom.:

15791

Cov.:

AF XY:

0.442

AC XY:

32848

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.608

AC:

25206

AN:

41442

American (AMR)

AF:

0.484

AC:

7407

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.369

AC:

1281

AN:

3470

East Asian (EAS)

AF:

0.596

AC:

3082

AN:

5172

South Asian (SAS)

AF:

0.384

AC:

1850

AN:

4812

European-Finnish (FIN)

AF:

0.398

AC:

4202

AN:

10548

Middle Eastern (MID)

AF:

0.320

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.324

AC:

22019

AN:

67972

Other (OTH)

AF:

0.460

AC:

970

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

1864

3729

5593

7458

9322

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

596

1192

1788

2384

2980

<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:

0.372

Hom.:

22322

Bravo

AF:

0.450

Asia WGS

AF:

0.521

AC:

1810

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

3.3

(source)

DANN

Benign

0.39

PhyloP100

0.39

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over