rs61737303

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_000149.4(FUT3):​c.975G>C​(p.Thr325Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Consequence

FUT3
NM_000149.4 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.64
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP7
Synonymous conserved (PhyloP=-1.64 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FUT3NM_000149.4 linkc.975G>C p.Thr325Thr synonymous_variant Exon 3 of 3 NP_000140.1 P21217A8K737
FUT3NM_001097639.3 linkc.975G>C p.Thr325Thr synonymous_variant Exon 3 of 3 NP_001091108.3 P21217A8K737
FUT3NM_001097640.3 linkc.975G>C p.Thr325Thr synonymous_variant Exon 3 of 3 NP_001091109.3 P21217A8K737

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FUT3ENST00000303225.12 linkc.975G>C p.Thr325Thr synonymous_variant Exon 3 of 3 1 ENSP00000305603.5 P21217
FUT3ENST00000458379.7 linkc.975G>C p.Thr325Thr synonymous_variant Exon 2 of 2 1 ENSP00000416443.1 P21217
FUT3ENST00000589620.6 linkc.975G>C p.Thr325Thr synonymous_variant Exon 3 of 3 1 ENSP00000465804.1 P21217
FUT3ENST00000589918.5 linkc.975G>C p.Thr325Thr synonymous_variant Exon 3 of 3 1 ENSP00000468123.1 P21217

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
34
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
0.34
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.

Other links and lift over

dbSNP: rs61737303; hg19: chr19-5843876; API