rs176452

Variant names:

• chrX-151397088-G-A
• rs176452
• NM_001363810.1:c.218+31G>A

Your query was ambiguous. Multiple possible variants found:

• chrX-151397088-G-A
• chrX-151397088-G-C
• chrX-151397088-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001363810.1(VMA21):​c.218+31G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 22)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: VMA21 NM_001363810.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68
• Publications: 2 publications found

Genes affected

VMA21 (HGNC:22082): (vacuolar ATPase assembly factor VMA21) This gene encodes a chaperone for assembly of lysosomal vacuolar ATPase.[provided by RefSeq, Jul 2012]

VMA21 Gene-Disease associations (from GenCC):

• X-linked myopathy with excessive autophagy

  Inheritance: XL Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

ENSG00000287918 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001363810.1. 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
	VMA21	NM_001363810.1		c.218+31G>A		intron	N/A	NP_001350739.1	Q3ZAQ7-2
	VMA21	NM_001017980.4	MANE Select	c.-221G>A		upstream_gene	N/A	NP_001017980.1	Q3ZAQ7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VMA21	ENST00000370361.5	TSL:5	c.218+31G>A		intron	N/A	ENSP00000359386.1	Q3ZAQ7-2
	ENSG00000287918	ENST00000660681.3		n.50C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000287918	ENST00000668689.1		n.55C>T		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 330775 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 105617

African (AFR) AF: 0.00 AC: 0 AN: 9159

American (AMR) AF: 0.00 AC: 0 AN: 16520

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10455

East Asian (EAS) AF: 0.00 AC: 0 AN: 21298

South Asian (SAS) AF: 0.00 AC: 0 AN: 26495

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 23309

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1435

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 202570

Other (OTH) AF: 0.00 AC: 0 AN: 19534

GnomAD4 genome Cov.: 22

Alfa AF: 0.00 Hom.: 3490

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.041
DANN	Benign	0.96
PhyloP100		-2.7
PromoterAI		-0.0098	Neutral

Splicing

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

Other links and lift over

dbSNP: rs176452; hg19: chrX-150565560;