rs776243191
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_001039958.2(MESP2):c.561_584delGCAGGGGCAAGGGCAGGGGCAAGG(p.Gln188_Gly195del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: not found (cov: 0)
Consequence
MESP2
NM_001039958.2 disruptive_inframe_deletion
NM_001039958.2 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.59
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 Likely_benign. Variant got -2 ACMG points.
BP6
Variant 15-89776915-GGGGCAGGGGCAAGGGCAGGGGCAA-G is Benign according to our data. Variant chr15-89776915-GGGGCAGGGGCAAGGGCAGGGGCAA-G is described in ClinVar as [Benign]. Clinvar id is 257244.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MESP2 | ENST00000341735.5 | c.561_584delGCAGGGGCAAGGGCAGGGGCAAGG | p.Gln188_Gly195del | disruptive_inframe_deletion | Exon 1 of 2 | 1 | NM_001039958.2 | ENSP00000342392.3 | ||
MESP2 | ENST00000560219.2 | c.31-1147_31-1124delGCAGGGGCAAGGGCAGGGGCAAGG | intron_variant | Intron 2 of 2 | 1 | ENSP00000452998.1 | ||||
MESP2 | ENST00000558723.1 | n.39-1147_39-1124delGCAGGGGCAAGGGCAGGGGCAAGG | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes Cov.: 0
GnomAD3 genomes
Cov.:
0
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 0
GnomAD4 genome
Cov.:
0
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
-
PreventionGenetics, part of Exact Sciences
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at