20-32210178-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015352.2(POFUT1):c.232C>T(p.Pro78Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,832 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P78P) has been classified as Likely benign.
Frequency
Consequence
NM_015352.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POFUT1 | NM_015352.2 | c.232C>T | p.Pro78Ser | missense_variant | Exon 2 of 7 | ENST00000375749.8 | NP_056167.1 | |
POFUT1 | NM_172236.2 | c.232C>T | p.Pro78Ser | missense_variant | Exon 2 of 5 | NP_758436.1 | ||
POFUT1 | XM_047440079.1 | c.-79+2113C>T | intron_variant | Intron 1 of 5 | XP_047296035.1 | |||
POFUT1 | XR_007067447.1 | n.294C>T | non_coding_transcript_exon_variant | Exon 2 of 6 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461832Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727226
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.