X-151397011-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001363810.1(VMA21):āc.172G>Cā(p.Glu58Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000505 in 514,846 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. 9/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001363810.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VMA21 | NM_001363810.1 | c.172G>C | p.Glu58Gln | 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.172G>C | p.Glu58Gln | missense_variant | Exon 2 of 4 | 5 | ENSP00000359386.1 | |||
ENSG00000287918 | ENST00000660681.2 | n.127C>G | non_coding_transcript_exon_variant | Exon 1 of 2 | ||||||
ENSG00000287918 | ENST00000664935.1 | n.8C>G | non_coding_transcript_exon_variant | Exon 1 of 2 |
Frequencies
GnomAD3 genomes AF: 0.0000629 AC: 7AN: 111240Hom.: 0 Cov.: 21 AF XY: 0.0000298 AC XY: 1AN XY: 33552
GnomAD3 exomes AF: 0.0000106 AC: 1AN: 94685Hom.: 0 AF XY: 0.0000295 AC XY: 1AN XY: 33927
GnomAD4 exome AF: 0.0000471 AC: 19AN: 403606Hom.: 0 Cov.: 0 AF XY: 0.0000408 AC XY: 6AN XY: 147160
GnomAD4 genome AF: 0.0000629 AC: 7AN: 111240Hom.: 0 Cov.: 21 AF XY: 0.0000298 AC XY: 1AN XY: 33552
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2022 | VMA21: PM2, BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at