chr1-172442125-A-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_153747.2(PIGC):āc.498T>Cā(p.Tyr166=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000783 in 1,614,244 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0043 ( 7 hom., cov: 32)
Exomes š: 0.00042 ( 6 hom. )
Consequence
PIGC
NM_153747.2 synonymous
NM_153747.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.207
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 -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
Variant 1-172442125-A-G is Benign according to our data. Variant chr1-172442125-A-G is described in ClinVar as [Benign]. Clinvar id is 767727.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.207 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00431 (657/152360) while in subpopulation AFR AF= 0.0146 (608/41590). AF 95% confidence interval is 0.0137. There are 7 homozygotes in gnomad4. There are 321 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGC | NM_153747.2 | c.498T>C | p.Tyr166= | synonymous_variant | 2/2 | ENST00000344529.5 | |
C1orf105 | NM_139240.4 | c.22-2948A>G | intron_variant | ENST00000367727.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGC | ENST00000344529.5 | c.498T>C | p.Tyr166= | synonymous_variant | 2/2 | 1 | NM_153747.2 | P1 | |
C1orf105 | ENST00000367727.9 | c.22-2948A>G | intron_variant | 1 | NM_139240.4 | P1 | |||
PIGC | ENST00000484368.1 | n.96+1863T>C | intron_variant, non_coding_transcript_variant | 1 | |||||
PIGC | ENST00000367728.1 | c.498T>C | p.Tyr166= | synonymous_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00428 AC: 651AN: 152242Hom.: 7 Cov.: 32
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GnomAD3 exomes AF: 0.00115 AC: 289AN: 251342Hom.: 2 AF XY: 0.000928 AC XY: 126AN XY: 135838
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GnomAD4 exome AF: 0.000415 AC: 607AN: 1461884Hom.: 6 Cov.: 40 AF XY: 0.000356 AC XY: 259AN XY: 727240
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GnomAD4 genome AF: 0.00431 AC: 657AN: 152360Hom.: 7 Cov.: 32 AF XY: 0.00431 AC XY: 321AN XY: 74512
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 12, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at