rs603985
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000511.6(FUT2):c.*12T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 1,607,326 control chromosomes in the GnomAD database, including 199,649 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 0.46 ( 17136 hom., cov: 32)
Exomes 𝑓: 0.49 ( 182513 hom. )
Consequence
FUT2
NM_000511.6 3_prime_UTR
NM_000511.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0270
Genes affected
FUT2 (HGNC:4013): (fucosyltransferase 2 (H blood group)) This gene is one of two encoding the galactoside 2-L-fucosyltransferase enzyme. The encoded protein is important for the final step in the soluble ABO blood group antigen synthesis pathway. It is also involved in cell-cell interaction, cell surface expression, and cell proliferation. Mutations in this gene are a cause of the H-Bombay blood group where red blood cells lack the H antigen. [provided by RefSeq, May 2022]
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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=-0.94).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FUT2 | NM_000511.6 | c.*12T>C | 3_prime_UTR_variant | 2/2 | ENST00000425340.3 | ||
FUT2 | NM_001097638.3 | c.*12T>C | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FUT2 | ENST00000425340.3 | c.*12T>C | 3_prime_UTR_variant | 2/2 | 1 | NM_000511.6 | P1 | ||
FUT2 | ENST00000522966.2 | c.*12T>C | 3_prime_UTR_variant | 2/2 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.462 AC: 69941AN: 151458Hom.: 17141 Cov.: 32
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GnomAD3 exomes AF: 0.403 AC: 100754AN: 249804Hom.: 23466 AF XY: 0.407 AC XY: 55016AN XY: 135236
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GnomAD4 exome AF: 0.486 AC: 707063AN: 1455752Hom.: 182513 Cov.: 36 AF XY: 0.480 AC XY: 347879AN XY: 724370
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GnomAD4 genome ? AF: 0.462 AC: 69952AN: 151574Hom.: 17136 Cov.: 32 AF XY: 0.449 AC XY: 33265AN XY: 74032
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at