rs776243191

chr15-89776915-GGGGCAGGGGCAAGGGCAGGGGCAA-Gchr15-89776915-GGGGCAGGGGCAAGGGCAGGGGCAA-GGGGCAGGGGCAAchr15-89776915-GGGGCAGGGGCAAGGGCAGGGGCAA-GGGGCAGGGGCAAGGGCAGGGGCAAGGGCAGGGGCAAchr15-89776915-GGGGCAGGGGCAAGGGCAGGGGCAA-GGGGCAGGGGCAAGGGCAGGGGCAAGGGCAGGGGCAAGGGCAGGGGCAA

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001039958.2(MESP2):c.561_584del(p.Gln198_Gly205del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. G187G) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 0)
• Consequence: MESP2 NM_001039958.2 inframe_deletion
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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]

ACMG classification

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

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MESP2	NM_001039958.2	c.561_584del	p.Gln198_Gly205del	inframe_deletion	1/2	ENST00000341735.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MESP2	ENST00000341735.5	c.561_584del	p.Gln198_Gly205del	inframe_deletion	1/2	1	NM_001039958.2	P1
MESP2	ENST00000560219.2	c.31-1147_31-1124del		intron_variant		1
MESP2	ENST00000558723.1	n.39-1147_39-1124del		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes Cov.: 0

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 0

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs776243191; hg19: chr15-90320146;