rs145997327
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 3P and 5B. PM2PM4_SupportingBP6BS1
The NM_013296.5(GPSM2):c.518_520delAAG(p.Glu173del) variant causes a disruptive inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000182 in 1,613,998 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_013296.5 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPSM2 | NM_013296.5 | c.518_520delAAG | p.Glu173del | disruptive_inframe_deletion | Exon 5 of 15 | ENST00000264126.9 | NP_037428.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000749 AC: 114AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000167 AC: 42AN: 251396Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135864
GnomAD4 exome AF: 0.000122 AC: 178AN: 1461750Hom.: 0 AF XY: 0.000109 AC XY: 79AN XY: 727188
GnomAD4 genome AF: 0.000762 AC: 116AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.000806 AC XY: 60AN XY: 74436
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
- -
In-frame deletion of 1 amino acid in a non-repeat region; In silico analysis supports a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
not specified Benign:1
The p.Glu173del variant in GPSM2 is classified as likely benign because it has been identified in 0.23% (58/24964) of African chromosomes by gnomAD (http://gnomad.broadinstitute.org), which is too common to cause Chudley-McCullough syndrome. ACMG/AMP criteria applied: BS1. -
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
GPSM2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at