9-136327739-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001145638.3(GPSM1):c.44C>T(p.Pro15Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000586 in 1,193,866 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145638.3 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 |
---|---|---|---|---|---|---|---|---|
GPSM1 | NM_001145638.3 | c.44C>T | p.Pro15Leu | missense_variant | Exon 1 of 14 | ENST00000440944.6 | NP_001139110.2 | |
GPSM1 | NM_015597.6 | c.44C>T | p.Pro15Leu | missense_variant | Exon 1 of 9 | NP_056412.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPSM1 | ENST00000440944.6 | c.44C>T | p.Pro15Leu | missense_variant | Exon 1 of 14 | 5 | NM_001145638.3 | ENSP00000392828.1 | ||
GPSM1 | ENST00000616132.4 | c.44C>T | p.Pro15Leu | missense_variant | Exon 1 of 9 | 1 | ENSP00000479405.1 |
Frequencies
GnomAD3 genomes AF: 0.0000199 AC: 3AN: 150614Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000383 AC: 4AN: 1043252Hom.: 0 Cov.: 22 AF XY: 0.00000402 AC XY: 2AN XY: 497596
GnomAD4 genome AF: 0.0000199 AC: 3AN: 150614Hom.: 0 Cov.: 33 AF XY: 0.0000136 AC XY: 1AN XY: 73522
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.44C>T (p.P15L) alteration is located in exon 1 (coding exon 1) of the GPSM1 gene. This alteration results from a C to T substitution at nucleotide position 44, causing the proline (P) at amino acid position 15 to be replaced by a leucine (L). 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