10-73250878-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016065.4(MRPS16):āc.388A>Gā(p.Thr130Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000682 in 1,614,062 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. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T130R) has been classified as Likely benign.
Frequency
Consequence
NM_016065.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRPS16 | NM_016065.4 | c.388A>G | p.Thr130Ala | missense_variant | 3/3 | ENST00000372945.8 | |
DNAJC9-AS1 | NR_038373.1 | n.175+2428T>C | intron_variant, non_coding_transcript_variant | ||||
MRPS16 | XM_047425263.1 | c.382A>G | p.Thr128Ala | missense_variant | 3/3 | ||
MRPS16 | NM_001410935.1 | c.274+885A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPS16 | ENST00000372945.8 | c.388A>G | p.Thr130Ala | missense_variant | 3/3 | 1 | NM_016065.4 | P1 | |
DNAJC9-AS1 | ENST00000440197.2 | n.182+2428T>C | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000722 AC: 11AN: 152252Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251446Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135900
GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461810Hom.: 0 Cov.: 31 AF XY: 0.0000633 AC XY: 46AN XY: 727214
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152252Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 18, 2023 | The c.388A>G (p.T130A) alteration is located in exon 3 (coding exon 3) of the MRPS16 gene. This alteration results from a A to G substitution at nucleotide position 388, causing the threonine (T) at amino acid position 130 to be replaced by an alanine (A). 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