chrX-3314658-C-A

Variant names:

• chrX-3314658-C-A
• rs1635239
• NM_015419.4:c.6578+2445G>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_015419.4(MXRA5):​c.6578+2445G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.61 (14654 hom., 18926 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: MXRA5 NM_015419.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202
• Publications: 3 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MXRA5	NM_015419.4	c.6578+2445G>T		intron_variant	Intron 6 of 6	ENST00000217939.7	NP_056234.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MXRA5	ENST00000217939.7	c.6578+2445G>T		intron_variant	Intron 6 of 6	5	NM_015419.4	ENSP00000217939.5

Frequencies

GnomAD3 genomes AF: 0.611 AC: 66328 AN: 108600 Hom.: 14667 Cov.: 21

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.621

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.610 AC: 66328 AN: 108659 Hom.: 14654 Cov.: 21 AF XY: 0.609 AC XY: 18926 AN XY: 31077

African (AFR) AF: 0.514 AC: 15298 AN: 29778

American (AMR) AF: 0.641 AC: 6522 AN: 10170

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 1587 AN: 2606

East Asian (EAS) AF: 0.737 AC: 2498 AN: 3389

South Asian (SAS) AF: 0.643 AC: 1551 AN: 2411

European-Finnish (FIN) AF: 0.643 AC: 3630 AN: 5642

Middle Eastern (MID) AF: 0.686 AC: 144 AN: 210

European-Non Finnish (NFE) AF: 0.645 AC: 33726 AN: 52308

Other (OTH) AF: 0.614 AC: 904 AN: 1473

Alfa AF: 0.629 Hom.: 5442

Bravo AF: 0.607

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.0
DANN	Benign	0.59
PhyloP100		-0.20
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1635239; hg19: chrX-3232699;