Genetic Variant MXRA5:p.Ala2622Ala (chrX-3310337-A-C) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_015419.4(MXRA5):c.7866T>G(p.Ala2622Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0279 in 1,162,238 control chromosomes in the GnomAD database, including 981 homozygotes. There are 13,183 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. A2622A) has been classified as Benign.

Frequency

Genomes: 𝑓 0.049 ( 121 hom., 1084 hem., cov: 22)

Exomes 𝑓: 0.026 ( 860 hom. 12099 hem. )

Consequence

MXRA5
NM_015419.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.97

Variant links:

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]

MXRA5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BP6

Variant X-3310337-A-C is Benign according to our data. Variant chrX-3310337-A-C is described in ClinVar as [Benign]. Clinvar id is 1333074.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.97 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MXRA5	NM_015419.4 link	c.7866T>G	p.Ala2622Ala	synonymous_variant	Exon 7 of 7	ENST00000217939.7	NP_056234.2	Q9NR99

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MXRA5	ENST00000217939.7 link	c.7866T>G	p.Ala2622Ala	synonymous_variant	Exon 7 of 7	5	NM_015419.4	ENSP00000217939.5		Q9NR99

Frequencies

GnomAD3 genomes

AF:

0.0493

AC:

5381

AN:

109150

Hom.:

121

Cov.:

AF XY:

0.0343

AC XY:

1084

AN XY:

31588

show subpopulations

Gnomad AFR

AF:

0.0684

Gnomad AMI

AF:

0.0665

Gnomad AMR

AF:

0.0339

Gnomad ASJ

AF:

0.0248

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0106

Gnomad FIN

AF:

0.0182

Gnomad MID

AF:

0.0795

Gnomad NFE

AF:

0.0510

Gnomad OTH

AF:

0.0404

GnomAD3 exomes

AF:

0.0171

AC:

3027

AN:

176626

Hom.:

AF XY:

0.0153

AC XY:

1009

AN XY:

65886

show subpopulations

Gnomad AFR exome

AF:

0.0417

Gnomad AMR exome

AF:

0.0119

Gnomad ASJ exome

AF:

0.00878

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00392

Gnomad FIN exome

AF:

0.00759

Gnomad NFE exome

AF:

0.0239

Gnomad OTH exome

AF:

0.0202

GnomAD4 exome

AF:

0.0257

AC:

27080

AN:

1053043

Hom.:

860

Cov.:

AF XY:

0.0338

AC XY:

12099

AN XY:

357983

show subpopulations

Gnomad4 AFR exome

AF:

0.0470

Gnomad4 AMR exome

AF:

0.0164

Gnomad4 ASJ exome

AF:

0.0196

Gnomad4 EAS exome

AF:

0.0000993

Gnomad4 SAS exome

AF:

0.00963

Gnomad4 FIN exome

AF:

0.0196

Gnomad4 NFE exome

AF:

0.0276

Gnomad4 OTH exome

AF:

0.0314

GnomAD4 genome

AF:

0.0493

AC:

5379

AN:

109195

Hom.:

121

Cov.:

AF XY:

0.0343

AC XY:

1084

AN XY:

31643

show subpopulations

Gnomad4 AFR

AF:

0.0683

Gnomad4 AMR

AF:

0.0339

Gnomad4 ASJ

AF:

0.0248

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0107

Gnomad4 FIN

AF:

0.0182

Gnomad4 NFE

AF:

0.0510

Gnomad4 OTH

AF:

0.0399

Alfa

AF:

0.0201

Hom.:

152

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jan 04, 2022

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.1

DANN

Benign

0.37

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over