chr9-136337933-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.790C>T(p.Arg264Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000552 in 1,611,512 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R264H) has been classified 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPSM1 | NM_001145638.3 | c.790C>T | p.Arg264Cys | missense_variant | 6/14 | ENST00000440944.6 | |
GPSM1 | NM_015597.6 | c.790C>T | p.Arg264Cys | missense_variant | 6/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPSM1 | ENST00000440944.6 | c.790C>T | p.Arg264Cys | missense_variant | 6/14 | 5 | NM_001145638.3 | P1 | |
GPSM1 | ENST00000616132.4 | c.790C>T | p.Arg264Cys | missense_variant | 6/9 | 1 | |||
GPSM1 | ENST00000354753.7 | c.886C>T | p.Arg296Cys | missense_variant | 6/14 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000985 AC: 15AN: 152230Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000149 AC: 37AN: 248410Hom.: 0 AF XY: 0.0000815 AC XY: 11AN XY: 134904
GnomAD4 exome AF: 0.0000507 AC: 74AN: 1459282Hom.: 0 Cov.: 31 AF XY: 0.0000372 AC XY: 27AN XY: 726002
GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152230Hom.: 0 Cov.: 34 AF XY: 0.000121 AC XY: 9AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.790C>T (p.R264C) alteration is located in exon 6 (coding exon 6) of the GPSM1 gene. This alteration results from a C to T substitution at nucleotide position 790, causing the arginine (R) at amino acid position 264 to be replaced by a cysteine (C). 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