chr1-172442230-A-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_153747.2(PIGC):c.393T>C(p.Tyr131=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00188 in 1,613,998 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0011 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0020 ( 3 hom. )
Consequence
PIGC
NM_153747.2 synonymous
NM_153747.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.881
Genes affected
PIGC (HGNC:8960): (phosphatidylinositol glycan anchor biosynthesis class C) This gene encodes an endoplasmic reticulum associated protein that is involved in glycosylphosphatidylinositol (GPI) lipid anchor biosynthesis. The GPI lipid anchor is a glycolipid found on many blood cells and serves to anchor proteins to the cell surface. The encoded protein is one subunit of the GPI N-acetylglucosaminyl (GlcNAc) transferase that transfers GlcNAc to phosphatidylinositol (PI) on the cytoplasmic side of the endoplasmic reticulum. Two alternatively spliced transcripts that encode the same protein have been found for this gene. A pseudogene on chromosome 11 has also been characterized. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 1-172442230-A-G is Benign according to our data. Variant chr1-172442230-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1299807.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-172442230-A-G is described in Lovd as [Likely_benign].
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00108 (164/152366) while in subpopulation NFE AF= 0.00191 (130/68036). AF 95% confidence interval is 0.00164. There are 1 homozygotes in gnomad4. There are 77 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGC | NM_153747.2 | c.393T>C | p.Tyr131= | synonymous_variant | 2/2 | ENST00000344529.5 | |
C1orf105 | NM_139240.4 | c.22-2843A>G | intron_variant | ENST00000367727.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGC | ENST00000344529.5 | c.393T>C | p.Tyr131= | synonymous_variant | 2/2 | 1 | NM_153747.2 | P1 | |
C1orf105 | ENST00000367727.9 | c.22-2843A>G | intron_variant | 1 | NM_139240.4 | P1 | |||
PIGC | ENST00000484368.1 | n.96+1758T>C | intron_variant, non_coding_transcript_variant | 1 | |||||
PIGC | ENST00000367728.1 | c.393T>C | p.Tyr131= | synonymous_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00107 AC: 163AN: 152248Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00108 AC: 272AN: 251032Hom.: 0 AF XY: 0.00113 AC XY: 153AN XY: 135742
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GnomAD4 exome AF: 0.00196 AC: 2863AN: 1461632Hom.: 3 Cov.: 40 AF XY: 0.00193 AC XY: 1402AN XY: 727086
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ClinVar
Significance: Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:4
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 19, 2023 | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | PIGC: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at