chr20-45416168-T-C
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_015937.6(PIGT):āc.12T>Cā(p.Ala4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000291 in 1,568,838 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.0016 ( 3 hom., cov: 33)
Exomes š: 0.00015 ( 3 hom. )
Consequence
PIGT
NM_015937.6 synonymous
NM_015937.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.20
Genes affected
PIGT (HGNC:14938): (phosphatidylinositol glycan anchor biosynthesis class T) 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 an essential component of the multisubunit enzyme, GPI transamidase. GPI transamidase mediates GPI anchoring in the endoplasmic reticulum, by catalyzing the transfer of fully assembled GPI units to proteins. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 20-45416168-T-C is Benign according to our data. Variant chr20-45416168-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 741217.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-5.2 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00159 (242/152368) while in subpopulation AFR AF= 0.00563 (234/41600). AF 95% confidence interval is 0.00503. There are 3 homozygotes in gnomad4. There are 117 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIGT | NM_015937.6 | c.12T>C | p.Ala4= | synonymous_variant | 1/12 | ENST00000279036.12 | NP_057021.2 | |
LOC107985405 | XR_001754640.2 | n.820A>G | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIGT | ENST00000279036.12 | c.12T>C | p.Ala4= | synonymous_variant | 1/12 | 1 | NM_015937.6 | ENSP00000279036 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00160 AC: 243AN: 152250Hom.: 3 Cov.: 33
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GnomAD3 exomes AF: 0.000317 AC: 56AN: 176830Hom.: 1 AF XY: 0.000301 AC XY: 29AN XY: 96258
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GnomAD4 exome AF: 0.000151 AC: 214AN: 1416470Hom.: 3 Cov.: 31 AF XY: 0.000130 AC XY: 91AN XY: 701156
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GnomAD4 genome AF: 0.00159 AC: 242AN: 152368Hom.: 3 Cov.: 33 AF XY: 0.00157 AC XY: 117AN XY: 74510
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
PIGT-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 17, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Multiple congenital anomalies-hypotonia-seizures syndrome 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 18, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 04, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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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