chr1-108924138-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS1
The NM_013296.5(GPSM2):c.1739C>T(p.Ser580Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000273 in 1,613,632 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_013296.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPSM2 | NM_013296.5 | c.1739C>T | p.Ser580Leu | missense_variant | Exon 14 of 15 | ENST00000264126.9 | NP_037428.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00137 AC: 208AN: 152048Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000422 AC: 106AN: 251288Hom.: 0 AF XY: 0.000353 AC XY: 48AN XY: 135798
GnomAD4 exome AF: 0.000156 AC: 228AN: 1461466Hom.: 1 Cov.: 31 AF XY: 0.000146 AC XY: 106AN XY: 727084
GnomAD4 genome AF: 0.00139 AC: 212AN: 152166Hom.: 1 Cov.: 32 AF XY: 0.00133 AC XY: 99AN XY: 74374
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
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The p.Ser580Leu variant (rs79730689) has not been reported in the medical literature. This variant is found in the Genome Aggregation Database (gnomAD) browser with an allele frequency of 0.47% in the African population (identified in 112 out of 24,016 chromosomes), and is listed in ClinVar with conflicting interpretations of pathogenicity (likely benign/uncertain significance; Variant ID: 178376). The serine at codon 580 is moderately conserved considering 12 species (Alamut software v2.9.0), and computational analyses predict conflicting effects of this variant on protein structure/function (SIFT: tolerated, PolyPhen2: benign, MutationTaster: disease causing). While this variant appears to be a benign polymorphism common in the African population, the available evidence is insufficient to classify the clinical significance of this variant with certainty. -
Chudley-McCullough syndrome Uncertain:1
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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
not specified Benign:1
Ser580Leu in exon 14 of GPSM2: This variant is not expected to have clinical sig nificance because it has been identified in 0.4% (19/4406) of African American c hromosomes from a broad population by the NHLBI Exome Sequencing Project (http:/ /evs.gs.washington.edu/EVS; dbSNP rs79730689). -
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