Variant X-3310622-G-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_015419.4(MXRA5):c.7581C>G(p.Ala2527=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 732,862 control chromosomes in the GnomAD database, including 46,361 homozygotes. There are 76,887 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.51 ( 10755 hom., 3882 hem., cov: 14)

Exomes 𝑓: 0.30 ( 46361 hom. 76887 hem. )

Failed GnomAD Quality Control

Consequence

MXRA5
NM_015419.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.108

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=-0.88).

BP6

Variant X-3310622-G-C is Benign according to our data. Variant chrX-3310622-G-C is described in ClinVar as [Benign]. Clinvar id is 1257846.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.108 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MXRA5	NM_015419.4 linkuse as main transcript	c.7581C>G	p.Ala2527=	synonymous_variant	7/7	ENST00000217939.7	NP_056234.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MXRA5	ENST00000217939.7 linkuse as main transcript	c.7581C>G	p.Ala2527=	synonymous_variant	7/7	5	NM_015419.4	ENSP00000217939	P1

Frequencies

GnomAD3 genomes

AF:

0.508

AC:

38326

AN:

75453

Hom.:

10767

Cov.:

AF XY:

0.236

AC XY:

3853

AN XY:

16359

show subpopulations

Gnomad AFR

AF:

0.612

Gnomad AMI

AF:

0.504

Gnomad AMR

AF:

0.464

Gnomad ASJ

AF:

0.460

Gnomad EAS

AF:

0.615

Gnomad SAS

AF:

0.413

Gnomad FIN

AF:

0.365

Gnomad MID

AF:

0.495

Gnomad NFE

AF:

0.467

Gnomad OTH

AF:

0.474

GnomAD3 exomes

AF:

0.212

AC:

22147

AN:

104366

Hom.:

5949

AF XY:

0.255

AC XY:

8769

AN XY:

34340

show subpopulations

Gnomad AFR exome

AF:

0.400

Gnomad AMR exome

AF:

0.287

Gnomad ASJ exome

AF:

0.116

Gnomad EAS exome

AF:

0.519

Gnomad SAS exome

AF:

0.239

Gnomad FIN exome

AF:

0.0307

Gnomad NFE exome

AF:

0.141

Gnomad OTH exome

AF:

0.257

GnomAD4 exome

AF:

0.297

AC:

217801

AN:

732862

Hom.:

46361

Cov.:

AF XY:

0.348

AC XY:

76887

AN XY:

221174

show subpopulations

Gnomad4 AFR exome

AF:

0.540

Gnomad4 AMR exome

AF:

0.442

Gnomad4 ASJ exome

AF:

0.397

Gnomad4 EAS exome

AF:

0.691

Gnomad4 SAS exome

AF:

0.461

Gnomad4 FIN exome

AF:

0.448

Gnomad4 NFE exome

AF:

0.233

Gnomad4 OTH exome

AF:

0.382

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.508

AC:

38330

AN:

75486

Hom.:

10755

Cov.:

AF XY:

0.237

AC XY:

3882

AN XY:

16406

show subpopulations

Gnomad4 AFR

AF:

0.612

Gnomad4 AMR

AF:

0.464

Gnomad4 ASJ

AF:

0.460

Gnomad4 EAS

AF:

0.614

Gnomad4 SAS

AF:

0.408

Gnomad4 FIN

AF:

0.365

Gnomad4 NFE

AF:

0.467

Gnomad4 OTH

AF:

0.466

Alfa

AF:

0.533

Hom.:

5122

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 20, 2020	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.3

DANN

Benign

0.42

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