rs5030799
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001905.4(CTPS1):āc.501A>Gā(p.Gln167=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0172 in 1,614,002 control chromosomes in the GnomAD database, including 628 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.022 ( 62 hom., cov: 32)
Exomes š: 0.017 ( 566 hom. )
Consequence
CTPS1
NM_001905.4 synonymous
NM_001905.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.742
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
?
Variant 1-40988656-A-G is Benign according to our data. Variant chr1-40988656-A-G is described in ClinVar as [Benign]. Clinvar id is 475187.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.742 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0852 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTPS1 | NM_001905.4 | c.501A>G | p.Gln167= | synonymous_variant | 5/19 | ENST00000650070.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTPS1 | ENST00000650070.2 | c.501A>G | p.Gln167= | synonymous_variant | 5/19 | NM_001905.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0220 AC: 3354AN: 152166Hom.: 64 Cov.: 32
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GnomAD3 exomes AF: 0.0254 AC: 6387AN: 251454Hom.: 175 AF XY: 0.0269 AC XY: 3659AN XY: 135900
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GnomAD4 exome AF: 0.0167 AC: 24433AN: 1461716Hom.: 566 Cov.: 30 AF XY: 0.0183 AC XY: 13283AN XY: 727162
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GnomAD4 genome ? AF: 0.0220 AC: 3356AN: 152286Hom.: 62 Cov.: 32 AF XY: 0.0232 AC XY: 1729AN XY: 74460
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Severe combined immunodeficiency due to CTPS1 deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at