NM_001017980.4:c.12G>A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001017980.4(VMA21):c.12G>A(p.Pro4Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000345 in 1,160,983 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001017980.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VMA21 | ENST00000330374.7 | c.12G>A | p.Pro4Pro | synonymous_variant | Exon 1 of 3 | 1 | NM_001017980.4 | ENSP00000333255.6 | ||
VMA21 | ENST00000370361.5 | c.218+263G>A | intron_variant | Intron 2 of 3 | 5 | ENSP00000359386.1 | ||||
VMA21 | ENST00000477649.1 | n.133+673G>A | intron_variant | Intron 1 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000883 AC: 1AN: 113229Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 35383
GnomAD4 exome AF: 0.00000286 AC: 3AN: 1047754Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 342126
GnomAD4 genome AF: 0.00000883 AC: 1AN: 113229Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 35383
ClinVar
Submissions by phenotype
X-linked myopathy with excessive autophagy Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at