Variant X-3310370-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7

The NM_015419.4(MXRA5):c.7833C>T(p.Ala2611=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.70 ( 19931 hom., 18927 hem., cov: 20)

Exomes 𝑓: 0.66 ( 158429 hom. 235163 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: -1.42

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant X-3310370-G-A is Benign according to our data. Variant chrX-3310370-G-A is described in ClinVar as [Benign]. Clinvar id is 1338966.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.42 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MXRA5	NM_015419.4 linkuse as main transcript	c.7833C>T	p.Ala2611=	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.7833C>T	p.Ala2611=	synonymous_variant	7/7	5	NM_015419.4	ENSP00000217939	P1

Frequencies

GnomAD3 genomes

AF:

0.697

AC:

73878

AN:

105972

Hom.:

19939

Cov.:

AF XY:

0.659

AC XY:

18888

AN XY:

28642

show subpopulations

Gnomad AFR

AF:

0.849

Gnomad AMI

AF:

0.700

Gnomad AMR

AF:

0.661

Gnomad ASJ

AF:

0.600

Gnomad EAS

AF:

0.718

Gnomad SAS

AF:

0.603

Gnomad FIN

AF:

0.594

Gnomad MID

AF:

0.680

Gnomad NFE

AF:

0.636

Gnomad OTH

AF:

0.689

GnomAD3 exomes

AF:

0.679

AC:

119486

AN:

176036

Hom.:

26571

AF XY:

0.673

AC XY:

42706

AN XY:

63446

show subpopulations

Gnomad AFR exome

AF:

0.860

Gnomad AMR exome

AF:

0.699

Gnomad ASJ exome

AF:

0.614

Gnomad EAS exome

AF:

0.770

Gnomad SAS exome

AF:

0.657

Gnomad FIN exome

AF:

0.656

Gnomad NFE exome

AF:

0.644

Gnomad OTH exome

AF:

0.656

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.655

AC:

712510

AN:

1087546

Hom.:

158429

Cov.:

AF XY:

0.652

AC XY:

235163

AN XY:

360480

show subpopulations

Gnomad4 AFR exome

AF:

0.858

Gnomad4 AMR exome

AF:

0.697

Gnomad4 ASJ exome

AF:

0.610

Gnomad4 EAS exome

AF:

0.758

Gnomad4 SAS exome

AF:

0.650

Gnomad4 FIN exome

AF:

0.645

Gnomad4 NFE exome

AF:

0.645

Gnomad4 OTH exome

AF:

0.664

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.697

AC:

73900

AN:

106012

Hom.:

19931

Cov.:

AF XY:

0.660

AC XY:

18927

AN XY:

28692

show subpopulations

Gnomad4 AFR

AF:

0.849

Gnomad4 AMR

AF:

0.662

Gnomad4 ASJ

AF:

0.600

Gnomad4 EAS

AF:

0.717

Gnomad4 SAS

AF:

0.600

Gnomad4 FIN

AF:

0.594

Gnomad4 NFE

AF:

0.636

Gnomad4 OTH

AF:

0.680

Alfa

AF:

0.666

Hom.:

7834

Bravo

AF:

0.719

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	Jan 29, 2022	- -
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

-0.85

CADD

Benign

0.045

DANN

Benign

0.47

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