X-151397033-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001363810.1(VMA21):āc.194G>Cā(p.Gly65Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000456 in 500,372 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 80 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 9/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001363810.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VMA21 | NM_001363810.1 | c.194G>C | p.Gly65Ala | missense_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.194G>C | p.Gly65Ala | missense_variant | Exon 2 of 4 | 5 | ENSP00000359386.1 | |||
ENSG00000287918 | ENST00000660681.2 | n.105C>G | non_coding_transcript_exon_variant | Exon 1 of 2 | ||||||
ENSG00000287918 | ENST00000668689.1 | n.110C>G | non_coding_transcript_exon_variant | Exon 1 of 2 |
Frequencies
GnomAD3 genomes AF: 0.000324 AC: 36AN: 111127Hom.: 0 Cov.: 21 AF XY: 0.000388 AC XY: 13AN XY: 33465
GnomAD3 exomes AF: 0.000781 AC: 66AN: 84537Hom.: 0 AF XY: 0.000608 AC XY: 16AN XY: 26317
GnomAD4 exome AF: 0.000493 AC: 192AN: 389198Hom.: 0 Cov.: 0 AF XY: 0.000489 AC XY: 67AN XY: 136978
GnomAD4 genome AF: 0.000324 AC: 36AN: 111174Hom.: 0 Cov.: 21 AF XY: 0.000388 AC XY: 13AN XY: 33520
ClinVar
Submissions by phenotype
VMA21-related disorder Benign:1
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
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Likely Benign. Following criteria are met: 0308 - Population frequency for this variant is out of keeping with known incidence of Myopathy, X-linked, with excessive autophagy (MIM#310440). (SB) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at