rs28462216
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001039958.2(MESP2):c.412G>A(p.Val138Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0127 in 1,531,108 control chromosomes in the GnomAD database, including 1,678 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001039958.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MESP2 | ENST00000341735.5 | c.412G>A | p.Val138Met | missense_variant | Exon 1 of 2 | 1 | NM_001039958.2 | ENSP00000342392.3 | ||
MESP2 | ENST00000560219.2 | c.31-1296G>A | intron_variant | Intron 2 of 2 | 1 | ENSP00000452998.1 | ||||
MESP2 | ENST00000558723.1 | n.39-1296G>A | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0610 AC: 9282AN: 152228Hom.: 901 Cov.: 33
GnomAD3 exomes AF: 0.0147 AC: 2266AN: 154542Hom.: 159 AF XY: 0.0131 AC XY: 1132AN XY: 86644
GnomAD4 exome AF: 0.00734 AC: 10124AN: 1378770Hom.: 778 Cov.: 30 AF XY: 0.00737 AC XY: 5020AN XY: 681270
GnomAD4 genome AF: 0.0610 AC: 9296AN: 152338Hom.: 900 Cov.: 33 AF XY: 0.0592 AC XY: 4408AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:3
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Spondylocostal dysostosis 2, autosomal recessive Benign:2
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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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at