1-108901820-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_013296.5(GPSM2):c.828A>G(p.Lys276Lys) variant causes a synonymous change. The variant allele was found at a frequency of 0.00515 in 1,612,284 control chromosomes in the GnomAD database, including 316 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_013296.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPSM2 | NM_013296.5 | c.828A>G | p.Lys276Lys | synonymous_variant | Exon 8 of 15 | ENST00000264126.9 | NP_037428.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0253 AC: 3846AN: 152156Hom.: 165 Cov.: 31
GnomAD3 exomes AF: 0.00744 AC: 1870AN: 251386Hom.: 66 AF XY: 0.00536 AC XY: 728AN XY: 135866
GnomAD4 exome AF: 0.00304 AC: 4444AN: 1460010Hom.: 150 Cov.: 29 AF XY: 0.00271 AC XY: 1968AN XY: 726520
GnomAD4 genome AF: 0.0253 AC: 3854AN: 152274Hom.: 166 Cov.: 31 AF XY: 0.0249 AC XY: 1854AN XY: 74460
ClinVar
Submissions by phenotype
not specified Benign:3
Lys276Lys in Exon 08 of GPSM2: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, and has been identified in 8.6% (320/3738) of A frican American chromosomes from a broad population by the NHLBI Exome Sequencin g Project (http://evs.gs.washington.edu/EVS; dbSNP rs338489). -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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not provided Benign:3
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Chudley-McCullough syndrome Benign:2
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at