4-165333383-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_006745.5(MSMO1):c.13G>C(p.Glu5Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000165 in 1,611,738 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E5D) has been classified as Uncertain significance.
Frequency
Consequence
NM_006745.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSMO1 | NM_006745.5 | c.13G>C | p.Glu5Gln | missense_variant | 2/6 | ENST00000261507.11 | |
MSMO1 | XM_005263176.3 | c.13G>C | p.Glu5Gln | missense_variant | 2/6 | ||
MSMO1 | NM_001017369.3 | c.-138-4406G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSMO1 | ENST00000261507.11 | c.13G>C | p.Glu5Gln | missense_variant | 2/6 | 1 | NM_006745.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000874 AC: 133AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000239 AC: 60AN: 251180Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135780
GnomAD4 exome AF: 0.0000911 AC: 133AN: 1459448Hom.: 0 Cov.: 31 AF XY: 0.0000799 AC XY: 58AN XY: 726032
GnomAD4 genome ? AF: 0.000873 AC: 133AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.000873 AC XY: 65AN XY: 74462
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 04, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at