Genetic Variant NM_001039958.2:c.573_584delGCAGGGGCAAGG (chr15-89776915-GGGGCAGGGGCAA-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001039958.2(MESP2):c.573_584delGCAGGGGCAAGG(p.Gln192_Gly195del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. G191G) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 0)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

MESP2
NM_001039958.2 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.59

Publications

0 publications found

Variant links:

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]

MESP2 Gene-Disease associations (from GenCC):

spondylocostal dysostosis 2, autosomal recessive
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
autosomal recessive spondylocostal dysostosis
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

MESP2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

BP6

Variant 15-89776915-GGGGCAGGGGCAA-G is Benign according to our data. Variant chr15-89776915-GGGGCAGGGGCAA-G is described in ClinVar as Benign. ClinVar VariationId is 257245.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039958.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MESP2	NM_001039958.2	MANE Select	c.573_584delGCAGGGGCAAGG	p.Gln192_Gly195del	disruptive_inframe_deletion	Exon 1 of 2	NP_001035047.1	Q0VG99

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MESP2	ENST00000341735.5	TSL:1 MANE Select	c.573_584delGCAGGGGCAAGG	p.Gln192_Gly195del	disruptive_inframe_deletion	Exon 1 of 2	ENSP00000342392.3	Q0VG99
MESP2	ENST00000560219.2	TSL:1	c.31-1135_31-1124delGCAGGGGCAAGG		intron	N/A	ENSP00000452998.1	H0YKZ5
MESP2	ENST00000558723.1	TSL:3	n.39-1135_39-1124delGCAGGGGCAAGG		intron	N/A

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

50908

Hom.:

AF XY:

0.00

AC XY:

AN XY:

24936

African (AFR)

AF:

0.00

AC:

AN:

9770

American (AMR)

AF:

0.00

AC:

AN:

1310

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

368

East Asian (EAS)

AF:

0.00

AC:

AN:

3194

South Asian (SAS)

AF:

0.00

AC:

AN:

4478

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1448

Middle Eastern (MID)

AF:

0.00

AC:

AN:

190

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

27366

Other (OTH)

AF:

0.00

AC:

AN:

2784

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.6

Mutation Taster

=190/10

polymorphism

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over