dbSNP rs34304528: FUT3:c.*189G>A (chr19-5843565-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_001097639.3(FUT3):c.*189G>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 0.101 in 1,109,484 control chromosomes in the GnomAD database, including 6,966 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 0.080 ( 652 hom., cov: 31)

Exomes 𝑓: 0.10 ( 6314 hom. )

Consequence

FUT3
NM_001097639.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.291

Publications

5 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:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_001097639.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.78).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 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	UniProt
FUT3	NM_001097639.3	MANE Select	c.*189G>A	3_prime_UTR	Exon 3 of 3	NP_001091108.3	A8K737
FUT3	NM_000149.4		c.*189G>A	3_prime_UTR	Exon 3 of 3	NP_000140.1	A8K737
FUT3	NM_001097640.3		c.*189G>A	3_prime_UTR	Exon 3 of 3	NP_001091109.3	A8K737

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FUT3	ENST00000303225.12	TSL:1	c.*189G>A	3_prime_UTR	Exon 3 of 3	ENSP00000305603.5	P21217
FUT3	ENST00000458379.7	TSL:1	c.*189G>A	3_prime_UTR	Exon 2 of 2	ENSP00000416443.1	P21217
FUT3	ENST00000589620.6	TSL:1	c.*189G>A	3_prime_UTR	Exon 3 of 3	ENSP00000465804.1	P21217

Frequencies

GnomAD3 genomes

AF:

0.0797

AC:

12111

AN:

151956

Hom.:

652

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0220

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.0678

Gnomad ASJ

AF:

0.0544

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0166

Gnomad FIN

AF:

0.105

Gnomad MID

AF:

0.0769

Gnomad NFE

AF:

0.124

Gnomad OTH

AF:

0.0818

GnomAD4 exome

AF:

0.104

AC:

99958

AN:

957410

Hom.:

6314

Cov.:

AF XY:

0.102

AC XY:

49524

AN XY:

487498

show subpopulations

African (AFR)

AF:

0.0187

AC:

440

AN:

23522

American (AMR)

AF:

0.0509

AC:

1655

AN:

32520

Ashkenazi Jewish (ASJ)

AF:

0.0611

AC:

1160

AN:

18992

East Asian (EAS)

AF:

0.000310

AC:

AN:

35514

South Asian (SAS)

AF:

0.0236

AC:

1516

AN:

64238

European-Finnish (FIN)

AF:

0.117

AC:

4061

AN:

34858

Middle Eastern (MID)

AF:

0.101

AC:

311

AN:

3076

European-Non Finnish (NFE)

AF:

0.124

AC:

86581

AN:

701022

Other (OTH)

AF:

0.0967

AC:

4223

AN:

43668

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

4693

9386

14078

18771

23464

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2512

5024

7536

10048

12560

<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:

0.0796

AC:

12107

AN:

152074

Hom.:

652

Cov.:

AF XY:

0.0769

AC XY:

5716

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.0219

AC:

910

AN:

41506

American (AMR)

AF:

0.0676

AC:

1032

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.0544

AC:

189

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5168

South Asian (SAS)

AF:

0.0162

AC:

AN:

4806

European-Finnish (FIN)

AF:

0.105

AC:

1109

AN:

10590

Middle Eastern (MID)

AF:

0.0828

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.124

AC:

8427

AN:

67958

Other (OTH)

AF:

0.0810

AC:

171

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

565

1130

1695

2260

2825

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

276

414

552

690

<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:

0.0863

Hom.:

Bravo

AF:

0.0774

Asia WGS

AF:

0.0140

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.92

(source)

DANN

Benign

0.81

PhyloP100

-0.29

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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