chr1-231241335-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_014236.4(GNPAT):c.-44C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 1,533,732 control chromosomes in the GnomAD database, including 236,756 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.55 ( 23102 hom., cov: 33)
Exomes 𝑓: 0.55 ( 213654 hom. )
Consequence
GNPAT
NM_014236.4 5_prime_UTR
NM_014236.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.132
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 1-231241335-C-T is Benign according to our data. Variant chr1-231241335-C-T is described in ClinVar as [Benign]. Clinvar id is 296108.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNPAT | NM_014236.4 | c.-44C>T | 5_prime_UTR_variant | 1/16 | ENST00000366647.9 | ||
GNPAT | NM_001316350.2 | c.-44C>T | 5_prime_UTR_variant | 1/15 | |||
GNPAT | XM_005273313.5 | c.-44C>T | 5_prime_UTR_variant | 1/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNPAT | ENST00000366647.9 | c.-44C>T | 5_prime_UTR_variant | 1/16 | 1 | NM_014236.4 | P1 | ||
GNPAT | ENST00000416000.1 | c.-44C>T | 5_prime_UTR_variant | 1/13 | 5 | ||||
GNPAT | ENST00000436239.5 | c.-44C>T | 5_prime_UTR_variant | 1/6 | 3 | ||||
GNPAT | ENST00000644483.1 | c.-44C>T | 5_prime_UTR_variant, NMD_transcript_variant | 1/17 |
Frequencies
GnomAD3 genomes AF: 0.549 AC: 83376AN: 151936Hom.: 23065 Cov.: 33
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GnomAD3 exomes AF: 0.554 AC: 138395AN: 249700Hom.: 38910 AF XY: 0.556 AC XY: 75079AN XY: 135086
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GnomAD4 exome AF: 0.553 AC: 764355AN: 1381678Hom.: 213654 Cov.: 22 AF XY: 0.555 AC XY: 384322AN XY: 692114
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GnomAD4 genome AF: 0.549 AC: 83456AN: 152054Hom.: 23102 Cov.: 33 AF XY: 0.544 AC XY: 40466AN XY: 74328
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Rhizomelic chondrodysplasia punctata type 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
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