17-4786216-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_182566.3(VMO1):āc.137A>Gā(p.Asp46Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,610,982 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_182566.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VMO1 | NM_182566.3 | c.137A>G | p.Asp46Gly | missense_variant | 1/3 | ENST00000328739.6 | NP_872372.1 | |
VMO1 | NM_001144939.2 | c.137A>G | p.Asp46Gly | missense_variant | 1/3 | NP_001138411.1 | ||
VMO1 | NM_001144940.2 | c.137A>G | p.Asp46Gly | missense_variant | 1/3 | NP_001138412.1 | ||
VMO1 | NM_001144941.2 | c.137A>G | p.Asp46Gly | missense_variant | 1/2 | NP_001138413.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VMO1 | ENST00000328739.6 | c.137A>G | p.Asp46Gly | missense_variant | 1/3 | 1 | NM_182566.3 | ENSP00000328397 | P1 | |
VMO1 | ENST00000354194.4 | c.137A>G | p.Asp46Gly | missense_variant | 1/2 | 1 | ENSP00000346133 | |||
VMO1 | ENST00000441199.2 | c.137A>G | p.Asp46Gly | missense_variant | 1/3 | 2 | ENSP00000408166 | |||
VMO1 | ENST00000416307.6 | c.137A>G | p.Asp46Gly | missense_variant | 1/3 | 2 | ENSP00000390450 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152162Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247558Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133934
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1458820Hom.: 0 Cov.: 80 AF XY: 0.0000124 AC XY: 9AN XY: 725474
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152162Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 06, 2022 | The c.137A>G (p.D46G) alteration is located in exon 1 (coding exon 1) of the VMO1 gene. This alteration results from a A to G substitution at nucleotide position 137, causing the aspartic acid (D) at amino acid position 46 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at