19-48703029-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000511.6(FUT2):c.73A>G(p.Ile25Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00694 in 1,613,032 control chromosomes in the GnomAD database, including 545 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.034 ( 275 hom., cov: 33)
Exomes 𝑓: 0.0041 ( 270 hom. )
Consequence
FUT2
NM_000511.6 missense
NM_000511.6 missense
Scores
15
Clinical Significance
Conservation
PhyloP100: -2.47
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0017546713).
BP6
?
Variant 19-48703029-A-G is Benign according to our data. Variant chr19-48703029-A-G is described in ClinVar as [Benign]. Clinvar id is 979159.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FUT2 | NM_000511.6 | c.73A>G | p.Ile25Val | missense_variant | 2/2 | ENST00000425340.3 | |
LOC105447645 | NR_131188.1 | n.820T>C | non_coding_transcript_exon_variant | 1/1 | |||
FUT2 | NM_001097638.3 | c.73A>G | p.Ile25Val | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FUT2 | ENST00000425340.3 | c.73A>G | p.Ile25Val | missense_variant | 2/2 | 1 | NM_000511.6 | P1 | |
FUT2 | ENST00000522966.2 | c.73A>G | p.Ile25Val | missense_variant | 2/2 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0335 AC: 5083AN: 151948Hom.: 263 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00933 AC: 2341AN: 250942Hom.: 114 AF XY: 0.00689 AC XY: 935AN XY: 135672
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GnomAD4 exome AF: 0.00415 AC: 6059AN: 1460968Hom.: 270 Cov.: 36 AF XY: 0.00364 AC XY: 2645AN XY: 726796
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GnomAD4 genome ? AF: 0.0337 AC: 5129AN: 152064Hom.: 275 Cov.: 33 AF XY: 0.0320 AC XY: 2375AN XY: 74314
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ESP6500AA
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523
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ExAC
?
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1369
Asia WGS
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35
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3418
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ClinVar
Significance: Benign
Submissions summary: Benign:1Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Fucosyltransferase 6 deficiency Benign:1
Benign, criteria provided, single submitter | research | Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard | - | The heterozygous p.Ile25Val variant in FUT2 has been identified in at least 1 individual from South Africa (PMID: 9760207). In vitro functional studies provide some evidence that the p.Ile25Val variant may not impact protein function (PMID: 9760207). However, these types of assays may not accurately represent biological function. This variant is classified as benign for fucosyltransferase deficiency because it has been identified in >10% of African chromosomes by ExAC (http://gnomad.broadinstitute.org/). - |
Familial Otitis Media Other:1
confers sensitivity, no assertion criteria provided | research | University of Washington Center for Mendelian Genomics, University of Washington | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
0.0090
.;B;B
Vest4
0.033, 0.020
MPC
0.15
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at