rs140668735
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS1
The NM_004204.5(PIGQ):c.1209C>T(p.Tyr403=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000799 in 1,608,740 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00049 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00083 ( 1 hom. )
Consequence
PIGQ
NM_004204.5 synonymous
NM_004204.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.561
Genes affected
PIGQ (HGNC:14135): (phosphatidylinositol glycan anchor biosynthesis class Q) This gene is involved in the first step 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 gene encodes a N-acetylglucosaminyl transferase component that is part of the complex that catalyzes transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to phosphatidylinositol (PI). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
?
Variant 16-578924-C-T is Benign according to our data. Variant chr16-578924-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 456028.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-578924-C-T is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=-0.561 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.000831 (1212/1458640) while in subpopulation NFE AF= 0.001 (1116/1110868). AF 95% confidence interval is 0.000955. There are 1 homozygotes in gnomad4_exome. There are 551 alleles in male gnomad4_exome subpopulation. Median coverage is 33. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGQ | NM_004204.5 | c.1209C>T | p.Tyr403= | synonymous_variant | 6/11 | ENST00000321878.10 | |
PIGQ | NM_148920.4 | c.1209C>T | p.Tyr403= | synonymous_variant | 6/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGQ | ENST00000321878.10 | c.1209C>T | p.Tyr403= | synonymous_variant | 6/11 | 1 | NM_004204.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000493 AC: 74AN: 149990Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000521 AC: 130AN: 249682Hom.: 0 AF XY: 0.000488 AC XY: 66AN XY: 135352
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GnomAD4 exome AF: 0.000831 AC: 1212AN: 1458640Hom.: 1 Cov.: 33 AF XY: 0.000759 AC XY: 551AN XY: 725688
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GnomAD4 genome ? AF: 0.000493 AC: 74AN: 150100Hom.: 1 Cov.: 33 AF XY: 0.000465 AC XY: 34AN XY: 73112
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
PIGQ-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 01, 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). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | PIGQ: BP4, BP7 - |
Epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
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
Splicing
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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