Genetic Variant FUT3:c.-206+65T>C (chr19-5851325-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001097639.3(FUT3):c.-206+65T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,772 control chromosomes in the GnomAD database, including 8,546 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 0.30 ( 8527 hom., cov: 29)

Exomes 𝑓: 0.35 ( 19 hom. )

Consequence

FUT3
NM_001097639.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.116

Publications

4 publications found

Variant links:

Genes affected

FUT3 (HGNC:4014): (fucosyltransferase 3 (Lewis blood group)) The Lewis histo-blood group system comprises a set of fucosylated glycosphingolipids that are synthesized by exocrine epithelial cells and circulate in body fluids. The glycosphingolipids function in embryogenesis, tissue differentiation, tumor metastasis, inflammation, and bacterial adhesion. They are secondarily absorbed to red blood cells giving rise to their Lewis phenotype. This gene is a member of the fucosyltransferase family, which catalyzes the addition of fucose to precursor polysaccharides in the last step of Lewis antigen biosynthesis. It encodes an enzyme with alpha(1,3)-fucosyltransferase and alpha(1,4)-fucosyltransferase activities. Mutations in this gene are responsible for the majority of Lewis antigen-negative phenotypes. Differences in the expression of this gene are associated with host susceptibility to viral infection. [provided by RefSeq, Aug 2020]

FUT3 links:

ENSG00000267709 (HGNC:):

ENSG00000267709 links:

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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=-0.96).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001097639.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FUT3	NM_001097639.3	MANE Select	c.-206+65T>C	intron	N/A	NP_001091108.3
FUT3	NM_000149.4		c.-554+65T>C	intron	N/A	NP_000140.1
FUT3	NM_001097640.3		c.-152+65T>C	intron	N/A	NP_001091109.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FUT3	ENST00000303225.12	TSL:1	c.-554+65T>C	intron	N/A	ENSP00000305603.5
FUT3	ENST00000458379.7	TSL:1	c.-13+65T>C	intron	N/A	ENSP00000416443.1
FUT3	ENST00000589620.6	TSL:1	c.-206+65T>C	intron	N/A	ENSP00000465804.1

Frequencies

GnomAD3 genomes

AF:

0.303

AC:

45921

AN:

151402

Hom.:

8524

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0892

Gnomad AMI

AF:

0.472

Gnomad AMR

AF:

0.262

Gnomad ASJ

AF:

0.320

Gnomad EAS

AF:

0.347

Gnomad SAS

AF:

0.356

Gnomad FIN

AF:

0.345

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.427

Gnomad OTH

AF:

0.280

GnomAD4 exome

AF:

0.353

AC:

AN:

252

Hom.:

AF XY:

0.361

AC XY:

AN XY:

144

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.250

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.167

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.313

AC:

AN:

Middle Eastern (MID)

AF:

0.125

AC:

AN:

European-Non Finnish (NFE)

AF:

0.443

AC:

AN:

106

Other (OTH)

AF:

0.321

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.542

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:

0.303

AC:

45923

AN:

151520

Hom.:

8527

Cov.:

AF XY:

0.299

AC XY:

22086

AN XY:

73954

show subpopulations

African (AFR)

AF:

0.0891

AC:

3685

AN:

41374

American (AMR)

AF:

0.263

AC:

4001

AN:

15236

Ashkenazi Jewish (ASJ)

AF:

0.320

AC:

1107

AN:

3462

East Asian (EAS)

AF:

0.347

AC:

1770

AN:

5100

South Asian (SAS)

AF:

0.357

AC:

1699

AN:

4758

European-Finnish (FIN)

AF:

0.345

AC:

3631

AN:

10512

Middle Eastern (MID)

AF:

0.262

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.427

AC:

28939

AN:

67776

Other (OTH)

AF:

0.279

AC:

586

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1425

2850

4274

5699

7124

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

472

944

1416

1888

2360

<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:

0.325

Hom.:

6155

Bravo

AF:

0.289

Asia WGS

AF:

0.286

AC:

993

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

2.2

(source)

DANN

Benign

0.23

PhyloP100

-0.12

PromoterAI

-0.084

Neutral

(source)

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