15-88465612-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022163.4(MRPL46):c.390G>T(p.Gln130His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,458,776 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_022163.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRPL46 | NM_022163.4 | c.390G>T | p.Gln130His | missense_variant | 2/4 | ENST00000312475.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPL46 | ENST00000312475.5 | c.390G>T | p.Gln130His | missense_variant | 2/4 | 1 | NM_022163.4 | P1 | |
MRPL46 | ENST00000558531.1 | c.390G>T | p.Gln130His | missense_variant | 2/2 | 2 | |||
MRPL46 | ENST00000558660.1 | n.136G>T | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
MRPL46 | ENST00000560703.1 | c.229-736G>T | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1458776Hom.: 0 Cov.: 30 AF XY: 0.00000276 AC XY: 2AN XY: 725666
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 14, 2023 | The c.390G>T (p.Q130H) alteration is located in exon 2 (coding exon 2) of the MRPL46 gene. This alteration results from a G to T substitution at nucleotide position 390, causing the glutamine (Q) at amino acid position 130 to be replaced by a histidine (H). 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