1-108896854-A-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_013296.5(GPSM2):c.57-10A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000837 in 1,588,394 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_013296.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPSM2 | NM_013296.5 | c.57-10A>G | intron_variant | Intron 2 of 14 | ENST00000264126.9 | NP_037428.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000875 AC: 22AN: 251382Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135874
GnomAD4 exome AF: 0.0000850 AC: 122AN: 1436072Hom.: 0 Cov.: 28 AF XY: 0.0000977 AC XY: 70AN XY: 716248
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:2
The c.57-10A>G variant in GPSM2 has not been previously reported in individuals with hearing loss or Chudley McCullough syndrome, but has been identified in 10/ 66552 European chromosomes by the Exome Aggregation Consortium (ExAC, http://exa c.broadinstitute.org; dbSNP rs184863735). This variant is located in the 3' spli ce region, but the adenine nucleotide (A) at position c.-10 is not well conserve d across species. In addition, computational tools do not suggest an impact to s plicing. However, this information is not predictive enough to rule out pathogen icity. In summary, while the clinical significance of the c.57-10A>G variant is uncertain, the conservation and computational data suggest that it is more likel y to be benign. -
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not provided Benign:2
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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