15-89776378-G-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001039958.2(MESP2):c.21G>T(p.Pro7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P7P) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MESP2
NM_001039958.2 synonymous
NM_001039958.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0940
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 -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 15-89776378-G-T is Benign according to our data. Variant chr15-89776378-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2117220.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.094 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| MESP2 | NM_001039958.2 | c.21G>T | p.Pro7= | synonymous_variant | 1/2 | ENST00000341735.5 | |
| LOC124903550 | XR_007064751.1 | n.232C>A | non_coding_transcript_exon_variant | 1/2 | |||
| LOC124903550 | XR_007064752.1 | n.197C>A | non_coding_transcript_exon_variant | 1/2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MESP2 | ENST00000341735.5 | c.21G>T | p.Pro7= | synonymous_variant | 1/2 | 1 | NM_001039958.2 | P1 | |
| MESP2 | ENST00000560219.2 | c.31-1687G>T | intron_variant | 1 | |||||
| MESP2 | ENST00000558723.1 | n.39-1687G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1379686Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 680942
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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0
AN:
1379686
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Cov.:
31
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0
AN XY:
680942
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GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
| Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 26, 2022 | - - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.