chr9-136337934-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001145638.3(GPSM1):c.791G>A(p.Arg264His) variant causes a missense change. The variant allele was found at a frequency of 0.000031 in 1,611,302 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict 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. R264C) 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPSM1 | NM_001145638.3 | c.791G>A | p.Arg264His | missense_variant | 6/14 | ENST00000440944.6 | |
GPSM1 | NM_015597.6 | c.791G>A | p.Arg264His | missense_variant | 6/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPSM1 | ENST00000440944.6 | c.791G>A | p.Arg264His | missense_variant | 6/14 | 5 | NM_001145638.3 | P1 | |
GPSM1 | ENST00000616132.4 | c.791G>A | p.Arg264His | missense_variant | 6/9 | 1 | |||
GPSM1 | ENST00000354753.7 | c.887G>A | p.Arg296His | missense_variant | 6/14 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152234Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000363 AC: 9AN: 248222Hom.: 0 AF XY: 0.0000519 AC XY: 7AN XY: 134834
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1459068Hom.: 1 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 725906
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152234Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 21, 2024 | The c.791G>A (p.R264H) alteration is located in exon 6 (coding exon 6) of the GPSM1 gene. This alteration results from a G to A substitution at nucleotide position 791, causing the arginine (R) at amino acid position 264 to be replaced by a histidine (H). 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