chr10-73250919-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016065.4(MRPS16):c.347G>T(p.Arg116Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,461,858 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 (★).
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.347G>T | p.Arg116Leu | missense_variant | 3/3 | ENST00000372945.8 | |
DNAJC9-AS1 | NR_038373.1 | n.175+2469C>A | intron_variant, non_coding_transcript_variant | ||||
MRPS16 | XM_047425263.1 | c.341G>T | p.Arg114Leu | missense_variant | 3/3 | ||
MRPS16 | NM_001410935.1 | c.274+844G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPS16 | ENST00000372945.8 | c.347G>T | p.Arg116Leu | missense_variant | 3/3 | 1 | NM_016065.4 | P1 | |
DNAJC9-AS1 | ENST00000440197.2 | n.182+2469C>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251478Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135918
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461858Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727232
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 30, 2021 | The c.347G>T (p.R116L) alteration is located in exon 3 (coding exon 3) of the MRPS16 gene. This alteration results from a G to T substitution at nucleotide position 347, causing the arginine (R) at amino acid position 116 to be replaced by a leucine (L). 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