chr19-48703304-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_000511.6(FUT2):c.348C>T(p.Ser116=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00237 in 1,612,992 control chromosomes in the GnomAD database, including 109 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 56 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 53 hom. )
Consequence
FUT2
NM_000511.6 synonymous
NM_000511.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.361
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 19-48703304-C-T is Benign according to our data. Variant chr19-48703304-C-T is described in ClinVar as [Benign]. Clinvar id is 3039160.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.361 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0127 (1935/152226) while in subpopulation AFR AF= 0.0444 (1847/41554). AF 95% confidence interval is 0.0428. There are 56 homozygotes in gnomad4. There are 915 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 56 BG gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FUT2 | NM_000511.6 | c.348C>T | p.Ser116= | synonymous_variant | 2/2 | ENST00000425340.3 | |
LOC105447645 | NR_131188.1 | n.545G>A | non_coding_transcript_exon_variant | 1/1 | |||
FUT2 | NM_001097638.3 | c.348C>T | p.Ser116= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FUT2 | ENST00000425340.3 | c.348C>T | p.Ser116= | synonymous_variant | 2/2 | 1 | NM_000511.6 | P1 | |
FUT2 | ENST00000522966.2 | c.348C>T | p.Ser116= | synonymous_variant | 2/2 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0127 AC: 1934AN: 152110Hom.: 56 Cov.: 32
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GnomAD3 exomes AF: 0.00320 AC: 797AN: 249248Hom.: 22 AF XY: 0.00238 AC XY: 322AN XY: 135206
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GnomAD4 exome AF: 0.00129 AC: 1882AN: 1460766Hom.: 53 Cov.: 67 AF XY: 0.00109 AC XY: 793AN XY: 726636
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GnomAD4 genome ? AF: 0.0127 AC: 1935AN: 152226Hom.: 56 Cov.: 32 AF XY: 0.0123 AC XY: 915AN XY: 74420
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
FUT2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 10, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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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