chr2-105038174-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_182640.3(MRPS9):c.82C>A(p.Gln28Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000089 in 1,461,230 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_182640.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MRPS9 | NM_182640.3 | c.82C>A | p.Gln28Lys | missense_variant | Exon 1 of 11 | ENST00000258455.8 | NP_872578.1 | |
MRPS9 | XM_047445533.1 | c.82C>A | p.Gln28Lys | missense_variant | Exon 1 of 7 | XP_047301489.1 | ||
MRPS9-AS2 | NR_110603.1 | n.43+280G>T | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1461230Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 726848
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.