rs2378199
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_080476.5(PIGU):c.628-10069A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 152,220 control chromosomes in the GnomAD database, including 52,946 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.83 ( 52946 hom., cov: 32)
Consequence
PIGU
NM_080476.5 intron
NM_080476.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.75
Genes affected
PIGU (HGNC:15791): (phosphatidylinositol glycan anchor biosynthesis class U) The protein encoded by this gene shares similarity with Saccharomyces cerevisiae Cdc91, a predicted integral membrane protein that may function in cell division control. The protein encoded by this gene is the fifth subunit of GPI transamidase that attaches GPI-anchors to proteins. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGU | NM_080476.5 | c.628-10069A>G | intron_variant | ENST00000217446.8 | |||
PIGU | XM_011528542.2 | c.-22+4454A>G | intron_variant | ||||
PIGU | XM_017027664.2 | c.628-10069A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGU | ENST00000217446.8 | c.628-10069A>G | intron_variant | 1 | NM_080476.5 | P1 | |||
PIGU | ENST00000374820.6 | c.568-10069A>G | intron_variant | 1 | |||||
PIGU | ENST00000438215.1 | c.53-10069A>G | intron_variant | 3 | |||||
PIGU | ENST00000480175.1 | n.90-10069A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.832 AC: 126526AN: 152102Hom.: 52891 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.832 AC: 126644AN: 152220Hom.: 52946 Cov.: 32 AF XY: 0.834 AC XY: 62066AN XY: 74432
GnomAD4 genome
?
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32
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62066
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74432
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2637
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at