chr18-62074825-G-GA
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_176787.5(PIGN):c.2577-5_2577-4insT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00697 in 1,565,040 control chromosomes in the GnomAD database, including 215 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0098 ( 41 hom., cov: 32)
Exomes 𝑓: 0.0067 ( 174 hom. )
Consequence
PIGN
NM_176787.5 splice_region, splice_polypyrimidine_tract, intron
NM_176787.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0730
Genes affected
PIGN (HGNC:8967): (phosphatidylinositol glycan anchor biosynthesis class N) This gene encodes a protein that is involved in glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor is a glycolipid found on many blood cells and serves to anchor proteins to the cell surface. This protein is expressed in the endoplasmic reticulum and transfers phosphoethanolamine (EtNP) to the first mannose of the GPI anchor. Two alternatively spliced variants, which encode an identical isoform, have been reported. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 18-62074825-G-GA is Benign according to our data. Variant chr18-62074825-G-GA is described in ClinVar as [Likely_benign]. Clinvar id is 472221.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0638 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGN | NM_176787.5 | c.2577-5_2577-4insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000640252.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGN | ENST00000640252.2 | c.2577-5_2577-4insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_176787.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00978 AC: 1467AN: 150064Hom.: 41 Cov.: 32
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GnomAD3 exomes AF: 0.0141 AC: 2956AN: 208964Hom.: 53 AF XY: 0.0140 AC XY: 1579AN XY: 113160
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GnomAD4 exome AF: 0.00668 AC: 9446AN: 1414862Hom.: 174 Cov.: 26 AF XY: 0.00652 AC XY: 4589AN XY: 704186
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GnomAD4 genome ? AF: 0.00976 AC: 1466AN: 150178Hom.: 41 Cov.: 32 AF XY: 0.0131 AC XY: 959AN XY: 73228
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Sep 18, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2018 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 24, 2017 | This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Multiple congenital anomalies-hypotonia-seizures syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
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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