1-40984816-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001905.4(CTPS1):c.167-5T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000162 in 1,547,318 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001905.4 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152258Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000350 AC: 8AN: 228482Hom.: 0 AF XY: 0.0000323 AC XY: 4AN XY: 123764
GnomAD4 exome AF: 0.0000151 AC: 21AN: 1395060Hom.: 0 Cov.: 30 AF XY: 0.0000189 AC XY: 13AN XY: 687214
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74388
ClinVar
Submissions by phenotype
Severe combined immunodeficiency due to CTPS1 deficiency Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at