rs141926826
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001017980.4(VMA21):āc.182A>Gā(p.Asn61Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000368 in 1,208,466 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 102 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. N61N) has been classified as Likely benign.
Frequency
Consequence
NM_001017980.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VMA21 | NM_001017980.4 | c.182A>G | p.Asn61Ser | missense_variant | 3/3 | ENST00000330374.7 | |
VMA21 | NM_001363810.1 | c.347A>G | p.Asn116Ser | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VMA21 | ENST00000330374.7 | c.182A>G | p.Asn61Ser | missense_variant | 3/3 | 1 | NM_001017980.4 | P1 | |
VMA21 | ENST00000370361.5 | c.347A>G | p.Asn116Ser | missense_variant | 4/4 | 5 | |||
VMA21 | ENST00000477649.1 | n.262A>G | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00188 AC: 208AN: 110477Hom.: 0 Cov.: 22 AF XY: 0.00147 AC XY: 48AN XY: 32675
GnomAD3 exomes AF: 0.000535 AC: 98AN: 183159Hom.: 0 AF XY: 0.000370 AC XY: 25AN XY: 67599
GnomAD4 exome AF: 0.000216 AC: 237AN: 1097937Hom.: 0 Cov.: 31 AF XY: 0.000149 AC XY: 54AN XY: 363311
GnomAD4 genome ? AF: 0.00188 AC: 208AN: 110529Hom.: 0 Cov.: 22 AF XY: 0.00147 AC XY: 48AN XY: 32737
ClinVar
Submissions by phenotype
VMA21-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 16, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
X-linked myopathy with excessive autophagy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 13, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at