rs199905093
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_014236.4(GNPAT):c.569-11del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 1,588,012 control chromosomes in the GnomAD database, including 125 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.0082 ( 12 hom., cov: 33)
Exomes 𝑓: 0.011 ( 113 hom. )
Consequence
GNPAT
NM_014236.4 splice_polypyrimidine_tract, intron
NM_014236.4 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.380
Genes affected
GNPAT (HGNC:4416): (glyceronephosphate O-acyltransferase) This gene encodes an enzyme located in the peroxisomal membrane which is essential to the synthesis of ether phospholipids. Mutations in this gene are associated with rhizomelic chondrodysplasia punctata. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP6
?
Variant 1-231265278-TC-T is Benign according to our data. Variant chr1-231265278-TC-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 211091.We mark this variant Likely_benign, oryginal submissions are: {Benign=4, Uncertain_significance=1}. Variant chr1-231265278-TC-T is described in Lovd as [Likely_benign].
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00822 (1252/152320) while in subpopulation NFE AF= 0.0115 (784/68016). AF 95% confidence interval is 0.0109. There are 12 homozygotes in gnomad4. There are 625 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 12 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNPAT | NM_014236.4 | c.569-11del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000366647.9 | |||
GNPAT | NM_001316350.2 | c.386-11del | splice_polypyrimidine_tract_variant, intron_variant | ||||
GNPAT | XM_005273313.5 | c.566-11del | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNPAT | ENST00000366647.9 | c.569-11del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_014236.4 | P1 | |||
GNPAT | ENST00000416000.1 | c.539-11del | splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
GNPAT | ENST00000436239.5 | c.386-11del | splice_polypyrimidine_tract_variant, intron_variant | 3 | |||||
GNPAT | ENST00000644483.1 | c.*255-11del | splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00822 AC: 1251AN: 152202Hom.: 12 Cov.: 33
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GnomAD3 exomes AF: 0.0101 AC: 2538AN: 251074Hom.: 22 AF XY: 0.0105 AC XY: 1433AN XY: 135864
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GnomAD4 exome AF: 0.0105 AC: 15127AN: 1435692Hom.: 113 Cov.: 28 AF XY: 0.0106 AC XY: 7596AN XY: 716250
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GnomAD4 genome ? AF: 0.00822 AC: 1252AN: 152320Hom.: 12 Cov.: 33 AF XY: 0.00839 AC XY: 625AN XY: 74482
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:5
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | GNPAT: BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Dec 16, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 16, 2016 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 21, 2014 | - - |
Rhizomelic chondrodysplasia punctata type 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 03, 2023 | - - |
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