rs12144160
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
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: 0.475 AC: 72202AN: 152020Hom.: 18608 Cov.: 32
GnomAD3 exomes AF: 0.537 AC: 101740AN: 189426Hom.: 28180 AF XY: 0.542 AC XY: 55063AN XY: 101548
GnomAD4 exome AF: 0.554 AC: 762470AN: 1375800Hom.: 213902 Cov.: 31 AF XY: 0.553 AC XY: 374383AN XY: 676886
GnomAD4 genome AF: 0.475 AC: 72255AN: 152140Hom.: 18617 Cov.: 32 AF XY: 0.478 AC XY: 35575AN XY: 74368
ClinVar
Submissions by phenotype
not specified Benign:1
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
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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