10-122980523-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001363531.2(PSTK):āc.44C>Gā(p.Pro15Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,609,244 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P15L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001363531.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PSTK | NM_001363531.2 | c.44C>G | p.Pro15Arg | missense_variant | Exon 1 of 6 | ENST00000406217.8 | NP_001350460.1 | |
PSTK | NM_153336.3 | c.44C>G | p.Pro15Arg | missense_variant | Exon 1 of 7 | NP_699167.2 | ||
PSTK | XM_017015641.3 | c.44C>G | p.Pro15Arg | missense_variant | Exon 1 of 4 | XP_016871130.1 | ||
PSTK | XR_001747018.2 | n.123C>G | non_coding_transcript_exon_variant | Exon 1 of 7 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000419 AC: 1AN: 238630Hom.: 0 AF XY: 0.00000762 AC XY: 1AN XY: 131240
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1457082Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 725000
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at