10-73250877-G-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_016065.4(MRPS16):āc.389C>Gā(p.Thr130Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00421 in 1,614,068 control chromosomes in the GnomAD database, including 22 homozygotes. 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 (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T130A) has been classified as Uncertain significance.
Frequency
Consequence
NM_016065.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRPS16 | NM_016065.4 | c.389C>G | p.Thr130Arg | missense_variant | 3/3 | ENST00000372945.8 | |
DNAJC9-AS1 | NR_038373.1 | n.175+2427G>C | intron_variant, non_coding_transcript_variant | ||||
MRPS16 | XM_047425263.1 | c.383C>G | p.Thr128Arg | missense_variant | 3/3 | ||
MRPS16 | NM_001410935.1 | c.274+886C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPS16 | ENST00000372945.8 | c.389C>G | p.Thr130Arg | missense_variant | 3/3 | 1 | NM_016065.4 | P1 | |
DNAJC9-AS1 | ENST00000440197.2 | n.182+2427G>C | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.00329 AC: 500AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00323 AC: 811AN: 251434Hom.: 3 AF XY: 0.00339 AC XY: 461AN XY: 135896
GnomAD4 exome AF: 0.00431 AC: 6299AN: 1461758Hom.: 22 Cov.: 31 AF XY: 0.00425 AC XY: 3087AN XY: 727198
GnomAD4 genome AF: 0.00328 AC: 500AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.00317 AC XY: 236AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | DNAJC9-AS1: BS2; MRPS16: BP4, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 21, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 22, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 29, 2016 | - - |
MRPS16-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 11, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at