MXRA7 p.Asp135Asp

Variant names:

• chr17-76688113-C-C
• NM_198530.4:c.

Your query was ambiguous. Multiple possible variants found:

• chr17-76688114--
• chr17-76688114-G-A

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_198530.4(MXRA7):​c. variant causes a splice region, exon region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MXRA7 NM_198530.4 splice_region, exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 0 publications found

Genes affected

MXRA7 (HGNC:7541): (matrix remodeling associated 7) Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

SNHG16 (HGNC:44352): (small nucleolar RNA host gene 16)

ENSG00000296346 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198530.4. 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
	MXRA7	NM_198530.4	MANE Select	c.		splice_region exon_region	Exon 2 of 4	NP_940932.2
	MXRA7	NM_001387276.1		c.		splice_region exon_region	Exon 1 of 3	NP_001374205.1
	MXRA7	NM_001387277.1		c.		splice_region exon_region	Exon 1 of 4	NP_001374206.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MXRA7	ENST00000449428.7	TSL:1 MANE Select	c.		splice_region exon_region	Exon 2 of 4	ENSP00000391466.1	P84157-2
	MXRA7	ENST00000592148.1	TSL:1	c.		splice_region exon_region	Exon 1 of 3	ENSP00000465103.1	Q6ZR64
	MXRA7	ENST00000355797.7	TSL:2	c.		splice_region exon_region	Exon 2 of 4	ENSP00000348050.2	P84157-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr17-74684195;