rs6579005
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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.588A>Gā(p.Pro196=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0108 in 1,613,994 control chromosomes in the GnomAD database, including 1,695 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.058 ( 913 hom., cov: 32)
Exomes š: 0.0059 ( 782 hom. )
Consequence
POFUT1
NM_015352.2 synonymous
NM_015352.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.82
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=-0.82).
BP6
?
Variant 20-32228308-A-G is Benign according to our data. Variant chr20-32228308-A-G is described in ClinVar as [Benign]. Clinvar id is 474295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-2.82 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POFUT1 | NM_015352.2 | c.588A>G | p.Pro196= | synonymous_variant | 5/7 | ENST00000375749.8 | |
LOC124904884 | XR_007067560.1 | n.940T>C | non_coding_transcript_exon_variant | 2/2 | |||
POFUT1 | XM_047440079.1 | c.264A>G | p.Pro88= | synonymous_variant | 4/6 | ||
POFUT1 | XR_007067447.1 | n.851A>G | non_coding_transcript_exon_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POFUT1 | ENST00000375749.8 | c.588A>G | p.Pro196= | synonymous_variant | 5/7 | 1 | NM_015352.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0579 AC: 8810AN: 152146Hom.: 908 Cov.: 32
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GnomAD3 exomes AF: 0.0147 AC: 3696AN: 251024Hom.: 332 AF XY: 0.0109 AC XY: 1474AN XY: 135676
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GnomAD4 exome AF: 0.00587 AC: 8585AN: 1461730Hom.: 782 Cov.: 31 AF XY: 0.00500 AC XY: 3633AN XY: 727176
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GnomAD4 genome ? AF: 0.0580 AC: 8833AN: 152264Hom.: 913 Cov.: 32 AF XY: 0.0557 AC XY: 4151AN XY: 74458
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Dowling-Degos disease 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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