17-3656510-TC-T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_004937.3(CTNS):c.486delC(p.Phe162LeufsTer4) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,170 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_004937.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTNS | NM_004937.3 | c.486delC | p.Phe162LeufsTer4 | frameshift_variant | Exon 8 of 12 | ENST00000046640.9 | NP_004928.2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 19
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461170Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726840
GnomAD4 genome Cov.: 19
ClinVar
Submissions by phenotype
Nephropathic cystinosis Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.