NM_001363810.1:c.180G>A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The NM_001363810.1(VMA21):c.180G>A(p.Arg60Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000237 in 506,282 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001363810.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VMA21 | NM_001363810.1 | c.180G>A | p.Arg60Arg | synonymous_variant | Exon 1 of 3 | NP_001350739.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VMA21 | ENST00000370361.5 | c.180G>A | p.Arg60Arg | synonymous_variant | Exon 2 of 4 | 5 | ENSP00000359386.1 | |||
ENSG00000287918 | ENST00000660681.2 | n.119C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | ||||||
ENSG00000287918 | ENST00000668689.1 | n.124C>T | non_coding_transcript_exon_variant | Exon 1 of 2 |
Frequencies
GnomAD3 genomes AF: 0.0000270 AC: 3AN: 111309Hom.: 0 Cov.: 21 AF XY: 0.0000595 AC XY: 2AN XY: 33599
GnomAD3 exomes AF: 0.0000335 AC: 3AN: 89658Hom.: 0 AF XY: 0.0000335 AC XY: 1AN XY: 29846
GnomAD4 exome AF: 0.0000228 AC: 9AN: 394973Hom.: 0 Cov.: 0 AF XY: 0.0000357 AC XY: 5AN XY: 140155
GnomAD4 genome AF: 0.0000270 AC: 3AN: 111309Hom.: 0 Cov.: 21 AF XY: 0.0000595 AC XY: 2AN XY: 33599
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: VMA21 c.-290G>A is located in the untranscribed region upstream of the VMA21 gene region. The variant was detected at a frequency of 4.5e-05 in 110157 control chromosomes, including 3 hemizygotes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.-290G>A in individuals affected with X-Linked Myopathy With Excessive Autophagy and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at