chr4-155942355-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001334.3(CTSO):c.346G>A(p.Asp116Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000522 in 1,588,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001334.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152048Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000131 AC: 3AN: 228480Hom.: 0 AF XY: 0.0000161 AC XY: 2AN XY: 124560
GnomAD4 exome AF: 0.0000564 AC: 81AN: 1436804Hom.: 0 Cov.: 30 AF XY: 0.0000685 AC XY: 49AN XY: 714862
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152048Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74254
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.346G>A (p.D116N) alteration is located in exon 3 (coding exon 3) of the CTSO gene. This alteration results from a G to A substitution at nucleotide position 346, causing the aspartic acid (D) at amino acid position 116 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at