chr1-206022174-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001910.4(CTSE):c.319G>A(p.Val107Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,076 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 8/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_001910.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTSE | NM_001910.4 | c.319G>A | p.Val107Met | missense_variant | 3/9 | ENST00000358184.7 | NP_001901.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CTSE | ENST00000358184.7 | c.319G>A | p.Val107Met | missense_variant | 3/9 | 1 | NM_001910.4 | ENSP00000350911.2 | ||
CTSE | ENST00000360218.3 | c.319G>A | p.Val107Met | missense_variant | 3/9 | 1 | ENSP00000353350.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249548Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134824
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459076Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 725888
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Malignant tumor of prostate Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | Science for Life laboratory, Karolinska Institutet | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at