rs28546919
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_001039958.2(MESP2):c.558G>A(p.Gln186=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. QGQGQG186QG) has been classified as Benign.
Frequency
Genomes: 𝑓 0.47 ( 617 hom., cov: 0)
Exomes 𝑓: 0.17 ( 677 hom. )
Failed GnomAD Quality Control
Consequence
MESP2
NM_001039958.2 synonymous
NM_001039958.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.36
Genes affected
MESP2 (HGNC:29659): (mesoderm posterior bHLH transcription factor 2) This gene encodes a member of the bHLH family of transcription factors and plays a key role in defining the rostrocaudal patterning of somites via interactions with multiple Notch signaling pathways. This gene is expressed in the anterior presomitic mesoderm and is downregulated immediately after the formation of segmented somites. This gene also plays a role in the formation of epithelial somitic mesoderm and cardiac mesoderm. Mutations in the MESP2 gene cause autosomal recessive spondylocostal dystosis 2 (SCD02). [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 15-89776915-G-A is Benign according to our data. Variant chr15-89776915-G-A is described in ClinVar as [Benign]. Clinvar id is 257243.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-89776915-G-A is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=-3.36 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MESP2 | NM_001039958.2 | c.558G>A | p.Gln186= | synonymous_variant | 1/2 | ENST00000341735.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MESP2 | ENST00000341735.5 | c.558G>A | p.Gln186= | synonymous_variant | 1/2 | 1 | NM_001039958.2 | P1 | |
MESP2 | ENST00000560219.2 | c.31-1150G>A | intron_variant | 1 | |||||
MESP2 | ENST00000558723.1 | n.39-1150G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 7540AN: 16080Hom.: 617 Cov.: 0 FAILED QC
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GnomAD3 exomes AF: 0.0253 AC: 1540AN: 60828Hom.: 234 AF XY: 0.0237 AC XY: 787AN XY: 33208
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.174 AC: 8831AN: 50886Hom.: 677 Cov.: 0 AF XY: 0.179 AC XY: 4454AN XY: 24926
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GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.469 AC: 7550AN: 16108Hom.: 617 Cov.: 0 AF XY: 0.469 AC XY: 3596AN XY: 7668
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Spondylocostal dysostosis 2, autosomal recessive Benign:2
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 26, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | 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
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at