rs12718433
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001905.4(CTPS1):c.1094+14G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 1,584,336 control chromosomes in the GnomAD database, including 136,227 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001905.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.351 AC: 53344AN: 151874Hom.: 10653 Cov.: 32
GnomAD3 exomes AF: 0.406 AC: 93307AN: 229616Hom.: 19733 AF XY: 0.405 AC XY: 50628AN XY: 124906
GnomAD4 exome AF: 0.414 AC: 593595AN: 1432344Hom.: 125572 Cov.: 27 AF XY: 0.412 AC XY: 293394AN XY: 712958
GnomAD4 genome AF: 0.351 AC: 53353AN: 151992Hom.: 10655 Cov.: 32 AF XY: 0.356 AC XY: 26466AN XY: 74272
ClinVar
Submissions by phenotype
not specified Benign:2
This variant is classified as Benign based on local population frequency. This variant was detected in 73% of patients studied by a panel of primary immunodeficiencies. Number of patients: 70. Only high quality variants are reported. -
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
Severe combined immunodeficiency due to CTPS1 deficiency Benign:2
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at