X-3310200-CGTCCCTGCCCAGCCCCG-TGTCCCTGCCCAGCTGCA

Position:

• chrX-3310200-CGTCCCTGCCCAGCCCCG-TGTCCCTGCCCAGCTGCA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_015419.4(MXRA5):​c.7986_8003delCGGGGCTGGGCAGGGACGinsTGCAGCTGGGCAGGGACA​(p.GlyAlaGlyGlnGlyArg2663AlaAlaGlyGlnGlyHis) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: not found (cov: 22)
• Consequence: MXRA5 NM_015419.4 missense
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 2.69

Genes affected

MXRA5 (HGNC:7539): (matrix remodeling associated 5) This gene encodes one of the matrix-remodelling associated proteins. This protein contains 7 leucine-rich repeats and 12 immunoglobulin-like C2-type domains related to perlecan. This gene has a pseudogene on chromosome Y. [provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MXRA5	NM_015419.4	c.7986_8003delCGGGGCTGGGCAGGGACGinsTGCAGCTGGGCAGGGACA	p.GlyAlaGlyGlnGlyArg2663AlaAlaGlyGlnGlyHis	missense_variant		ENST00000217939.7	NP_056234.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MXRA5	ENST00000217939.7	c.7986_8003delCGGGGCTGGGCAGGGACGinsTGCAGCTGGGCAGGGACA	p.GlyAlaGlyGlnGlyArg2663AlaAlaGlyGlnGlyHis	missense_variant		5	NM_015419.4	ENSP00000217939.5

Frequencies

GnomAD3 genomes Cov.: 22

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

GnomAD4 genome Cov.: 22

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

not provided, no classification provided

phenotyping only

GenomeConnect, ClinGen

-

Variant interpretted as Uncertain significance and reported on 06/15/2017 by GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

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: rs1603467724; hg19: chrX-3228241;