1-41009413-A-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001905.4(CTPS1):c.1547-32A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 1,527,940 control chromosomes in the GnomAD database, including 232,519 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.47 ( 18617 hom., cov: 32)
Exomes 𝑓: 0.55 ( 213902 hom. )
Consequence
CTPS1
NM_001905.4 intron
NM_001905.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.823
Genes affected
CTPS1 (HGNC:2519): (CTP synthase 1) This gene encodes an enzyme responsible for the catalytic conversion of UTP (uridine triphosphate) to CTP (cytidine triphospate). This reaction is an important step in the biosynthesis of phospholipids and nucleic acids. Activity of this proten is important in the immune system, and loss of function of this gene has been associated with immunodeficiency. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
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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=-0.89).
BP6
Variant 1-41009413-A-G is Benign according to our data. Variant chr1-41009413-A-G is described in ClinVar as [Benign]. Clinvar id is 1255416.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTPS1 | NM_001905.4 | c.1547-32A>G | intron_variant | ENST00000650070.2 | NP_001896.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CTPS1 | ENST00000650070.2 | c.1547-32A>G | intron_variant | NM_001905.4 | ENSP00000497602 | P1 |
Frequencies
GnomAD3 genomes AF: 0.475 AC: 72202AN: 152020Hom.: 18608 Cov.: 32
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GnomAD3 exomes AF: 0.537 AC: 101740AN: 189426Hom.: 28180 AF XY: 0.542 AC XY: 55063AN XY: 101548
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GnomAD4 exome AF: 0.554 AC: 762470AN: 1375800Hom.: 213902 Cov.: 31 AF XY: 0.553 AC XY: 374383AN XY: 676886
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GnomAD4 genome AF: 0.475 AC: 72255AN: 152140Hom.: 18617 Cov.: 32 AF XY: 0.478 AC XY: 35575AN XY: 74368
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Nov 12, 2023 | This variant is classified as Benign based on local population frequency. This variant was detected in 78% of patients studied by a panel of primary immunodeficiencies. Number of patients: 75. Only high quality variants are reported. - |
Severe combined immunodeficiency due to CTPS1 deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at