rs146017753
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001017980.4(VMA21):c.165C>T(p.Gly55=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00178 in 1,203,457 control chromosomes in the GnomAD database, including 1 homozygotes. There are 703 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001017980.4 splice_region, 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VMA21 | NM_001017980.4 | c.165C>T | p.Gly55= | splice_region_variant, synonymous_variant | 3/3 | ENST00000330374.7 | |
VMA21 | NM_001363810.1 | c.330C>T | p.Gly110= | splice_region_variant, synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VMA21 | ENST00000330374.7 | c.165C>T | p.Gly55= | splice_region_variant, synonymous_variant | 3/3 | 1 | NM_001017980.4 | P1 | |
VMA21 | ENST00000370361.5 | c.330C>T | p.Gly110= | splice_region_variant, synonymous_variant | 4/4 | 5 | |||
VMA21 | ENST00000477649.1 | n.245C>T | splice_region_variant, non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000949 AC: 102AN: 107492Hom.: 0 Cov.: 22 AF XY: 0.000758 AC XY: 23AN XY: 30348
GnomAD3 exomes AF: 0.000966 AC: 175AN: 181188Hom.: 0 AF XY: 0.00109 AC XY: 72AN XY: 65898
GnomAD4 exome AF: 0.00186 AC: 2036AN: 1095932Hom.: 1 Cov.: 31 AF XY: 0.00188 AC XY: 680AN XY: 361618
GnomAD4 genome ? AF: 0.000949 AC: 102AN: 107525Hom.: 0 Cov.: 22 AF XY: 0.000757 AC XY: 23AN XY: 30391
ClinVar
Submissions by phenotype
X-linked myopathy with excessive autophagy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at