rs878854352
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP3
The NM_001017980.4(VMA21):c.54-27A>C variant causes a intron 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 Uncertain significance (★).
Frequency
Genomes: not found (cov: 24)
Consequence
VMA21
NM_001017980.4 intron
NM_001017980.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.453
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PP3
?
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VMA21 | NM_001017980.4 | c.54-27A>C | intron_variant | ENST00000330374.7 | |||
VMA21 | NM_001363810.1 | c.219-27A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VMA21 | ENST00000330374.7 | c.54-27A>C | intron_variant | 1 | NM_001017980.4 | P1 | |||
VMA21 | ENST00000370361.5 | c.219-27A>C | intron_variant | 5 | |||||
VMA21 | ENST00000477649.1 | n.134-27A>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 24
GnomAD3 genomes
?
Cov.:
24
GnomAD4 exome Cov.: 20
GnomAD4 exome
Cov.:
20
GnomAD4 genome ? Cov.: 24
GnomAD4 genome
?
Cov.:
24
ClinVar
Significance: Uncertain significance
Submissions summary: Pathogenic:1Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
X-linked myopathy with excessive autophagy Pathogenic:1Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jul 01, 2021 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing, but this prediction has not been confirmed by published transcriptional studies. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on VMA21 protein function (PMID: 23315026). This variant has been observed in individual(s) with X-linked myopathy with excessive autophagy (PMID: 23315026). ClinVar contains an entry for this variant (Variation ID: 208798). This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 1 of the VMA21 gene. It does not directly change the encoded amino acid sequence of the VMA21 protein. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 01, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
La Branchor
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: 27
Find out detailed SpliceAI scores and Pangolin per-transcript scores at