chr20-32208016-T-C
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_015352.2(POFUT1):āc.75T>Cā(p.Pro25=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 1,580,522 control chromosomes in the GnomAD database, including 286,387 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.68 ( 37650 hom., cov: 33)
Exomes š: 0.58 ( 248737 hom. )
Consequence
POFUT1
NM_015352.2 synonymous
NM_015352.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.987
Genes affected
POFUT1 (HGNC:14988): (protein O-fucosyltransferase 1) This gene encodes a member of the glycosyltransferase O-Fuc family. This enzyme adds O-fucose through an O-glycosidic linkage to conserved serine or threonine residues in the epidermal growth factor-like repeats of a number of cell surface and secreted proteins. O-fucose glycans are involved in ligand-induced receptor signaling. Alternative splicing of this gene results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 20-32208016-T-C is Benign according to our data. Variant chr20-32208016-T-C is described in ClinVar as [Benign]. Clinvar id is 683580.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.987 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POFUT1 | NM_015352.2 | c.75T>C | p.Pro25= | synonymous_variant | 1/7 | ENST00000375749.8 | NP_056167.1 | |
POFUT1 | NM_172236.2 | c.75T>C | p.Pro25= | synonymous_variant | 1/5 | NP_758436.1 | ||
POFUT1 | XM_047440079.1 | c.-128T>C | 5_prime_UTR_variant | 1/6 | XP_047296035.1 | |||
POFUT1 | XR_007067447.1 | n.137T>C | non_coding_transcript_exon_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
POFUT1 | ENST00000375749.8 | c.75T>C | p.Pro25= | synonymous_variant | 1/7 | 1 | NM_015352.2 | ENSP00000364902 | P1 |
Frequencies
GnomAD3 genomes AF: 0.685 AC: 104031AN: 151976Hom.: 37578 Cov.: 33
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GnomAD3 exomes AF: 0.646 AC: 124513AN: 192886Hom.: 42375 AF XY: 0.623 AC XY: 66083AN XY: 106034
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GnomAD4 exome AF: 0.581 AC: 830173AN: 1428426Hom.: 248737 Cov.: 45 AF XY: 0.575 AC XY: 407885AN XY: 708754
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GnomAD4 genome AF: 0.685 AC: 104163AN: 152096Hom.: 37650 Cov.: 33 AF XY: 0.687 AC XY: 51062AN XY: 74352
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Dowling-Degos disease 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Oct 25, 2021 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
POFUT1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 02, 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
RBP_binding_hub_radar
RBP_regulation_power_radar
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