chr1-206012317-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001910.4(CTSE):c.1017C>T(p.Tyr339=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00213 in 1,613,110 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0017 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0022 ( 21 hom. )
Consequence
CTSE
NM_001910.4 synonymous
NM_001910.4 synonymous
Scores
1
6
Clinical Significance
Conservation
PhyloP100: 2.78
Genes affected
CTSE (HGNC:2530): (cathepsin E) This gene encodes a member of the A1 family of peptidases. Alternative splicing of this gene results in multiple transcript variants. At least one of these variants encodes a preproprotein that is proteolytically processed to generate the mature enzyme. This enzyme, an aspartic endopeptidase, may be involved in antigen processing and the maturation of secretory proteins. Elevated expression of this gene has been observed in neurodegeneration. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.028101772).
BP6
?
Variant 1-206012317-G-A is Benign according to our data. Variant chr1-206012317-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3078756.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.78 with no splicing effect.
BS2
?
High Homozygotes in GnomAdExome at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTSE | NM_001910.4 | c.1017C>T | p.Tyr339= | synonymous_variant | 8/9 | ENST00000358184.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTSE | ENST00000358184.7 | c.1017C>T | p.Tyr339= | synonymous_variant | 8/9 | 1 | NM_001910.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00172 AC: 262AN: 152180Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00163 AC: 408AN: 250996Hom.: 2 AF XY: 0.00161 AC XY: 219AN XY: 135650
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GnomAD4 exome AF: 0.00217 AC: 3167AN: 1460812Hom.: 21 Cov.: 31 AF XY: 0.00213 AC XY: 1551AN XY: 726786
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GnomAD4 genome ? AF: 0.00172 AC: 262AN: 152298Hom.: 1 Cov.: 33 AF XY: 0.00157 AC XY: 117AN XY: 74460
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 20, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
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Name
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BayesDel_noAF
Pathogenic
Cadd
Benign
Dann
Benign
LIST_S2
Benign
T
MetaRNN
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T
PROVEAN
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N
Sift
Benign
D
Sift4G
Benign
T
Vest4
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at