Variant rs34304528 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001382749.2(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_001382749.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.291

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FUT3	NM_001097639.3 linkuse as main transcript	c.*189G>A		3_prime_UTR_variant	3/3	ENST00000709635.1
FUT3	NM_001382749.2 linkuse as main transcript	c.*189G>A		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	Appris
FUT3	ENST00000303225.12 linkuse as main transcript	c.*189G>A	3_prime_UTR_variant	3/3	1	P1
FUT3	ENST00000458379.7 linkuse as main transcript	c.*189G>A	3_prime_UTR_variant	2/2	1	P1
FUT3	ENST00000589620.6 linkuse as main transcript	c.*189G>A	3_prime_UTR_variant	3/3	1	P1
FUT3	ENST00000589918.5 linkuse as main transcript	c.*189G>A	3_prime_UTR_variant	3/3	1	P1

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

Gnomad4 AFR exome

AF:

0.0187

Gnomad4 AMR exome

AF:

0.0509

Gnomad4 ASJ exome

AF:

0.0611

Gnomad4 EAS exome

AF:

0.000310

Gnomad4 SAS exome

AF:

0.0236

Gnomad4 FIN exome

AF:

0.117

Gnomad4 NFE exome

AF:

0.124

Gnomad4 OTH exome

AF:

0.0967

GnomAD4 genome

AF:

0.0796

AC:

12107

AN:

152074

Hom.:

652

Cov.:

AF XY:

0.0769

AC XY:

5716

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.0219

Gnomad4 AMR

AF:

0.0676

Gnomad4 ASJ

AF:

0.0544

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0162

Gnomad4 FIN

AF:

0.105

Gnomad4 NFE

AF:

0.124

Gnomad4 OTH

AF:

0.0810

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.92

DANN

Benign

0.81

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over