chr19-48703267-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_000511.6(FUT2):c.311C>T(p.Ala104Val) variant causes a missense change. The variant allele was found at a frequency of 0.00187 in 1,613,000 control chromosomes in the GnomAD database, including 115 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as confers sensitivity (no stars).
Frequency
Genomes: 𝑓 0.0013 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0019 ( 112 hom. )
Consequence
FUT2
NM_000511.6 missense
NM_000511.6 missense
Scores
6
6
6
Clinical Significance
Conservation
PhyloP100: 4.73
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 -9 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.01712045).
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0013 (198/152208) while in subpopulation SAS AF= 0.0194 (92/4738). AF 95% confidence interval is 0.0162. There are 3 homozygotes in gnomad4. There are 101 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High Homozygotes in GnomAd4 at 3 BG gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FUT2 | NM_000511.6 | c.311C>T | p.Ala104Val | missense_variant | 2/2 | ENST00000425340.3 | |
LOC105447645 | NR_131188.1 | n.582G>A | non_coding_transcript_exon_variant | 1/1 | |||
FUT2 | NM_001097638.3 | c.311C>T | p.Ala104Val | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FUT2 | ENST00000425340.3 | c.311C>T | p.Ala104Val | missense_variant | 2/2 | 1 | NM_000511.6 | P1 | |
FUT2 | ENST00000522966.2 | c.311C>T | p.Ala104Val | missense_variant | 2/2 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00130 AC: 198AN: 152092Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00352 AC: 872AN: 247802Hom.: 42 AF XY: 0.00444 AC XY: 598AN XY: 134642
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GnomAD4 exome AF: 0.00193 AC: 2820AN: 1460792Hom.: 112 Cov.: 67 AF XY: 0.00254 AC XY: 1845AN XY: 726648
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GnomAD4 genome AF: 0.00130 AC: 198AN: 152208Hom.: 3 Cov.: 32 AF XY: 0.00136 AC XY: 101AN XY: 74414
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ClinVar
Significance: confers sensitivity
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
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
Uncertain
T
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Pathogenic
DEOGEN2
Benign
.;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
.;.;D
MetaRNN
Benign
T;T;T
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
.;M;M
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D
REVEL
Pathogenic
Sift
Benign
D;T;T
Sift4G
Uncertain
D;T;T
Polyphen
1.0
.;D;D
Vest4
0.56, 0.82
MVP
MPC
0.73
ClinPred
T
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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