20-34581533-G-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_080476.5(PIGU):c.1051+15C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000275 in 1,454,674 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
PIGU
NM_080476.5 intron
NM_080476.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.27
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 Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 20-34581533-G-A is Benign according to our data. Variant chr20-34581533-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2976990.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIGU | NM_080476.5 | c.1051+15C>T | intron_variant | ENST00000217446.8 | NP_536724.1 | |||
PIGU | XM_011528542.2 | c.403+15C>T | intron_variant | XP_011526844.1 | ||||
PIGU | XM_017027664.2 | c.907+15C>T | intron_variant | XP_016883153.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIGU | ENST00000217446.8 | c.1051+15C>T | intron_variant | 1 | NM_080476.5 | ENSP00000217446 | P1 | |||
PIGU | ENST00000374820.6 | c.991+15C>T | intron_variant | 1 | ENSP00000363953 | |||||
PIGU | ENST00000438215.1 | c.289+15C>T | intron_variant | 3 | ENSP00000395755 | |||||
PIGU | ENST00000480175.1 | n.369+15C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.0000124 AC: 3AN: 241084Hom.: 0 AF XY: 0.00000765 AC XY: 1AN XY: 130690
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GnomAD4 exome AF: 0.00000275 AC: 4AN: 1454674Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 723546
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GnomAD4 genome Cov.: 32
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 09, 2023 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at