17-57839911-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000313608.13(MRPS23):c.445C>T(p.Arg149Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,614,138 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000313608.13 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MRPS23 | NM_016070.4 | c.445C>T | p.Arg149Trp | missense_variant | 5/5 | ENST00000313608.13 | NP_057154.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MRPS23 | ENST00000313608.13 | c.445C>T | p.Arg149Trp | missense_variant | 5/5 | 1 | NM_016070.4 | ENSP00000320184.8 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152150Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000636 AC: 16AN: 251470Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135908
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461872Hom.: 0 Cov.: 30 AF XY: 0.0000358 AC XY: 26AN XY: 727232
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74440
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at