19-38932427-G-T
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_033362.4(MRPS12):c.144G>T(p.Lys48Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000548 in 1,458,604 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K48R) has been classified as Uncertain significance.
Frequency
Consequence
NM_033362.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Our verdict: Likely_benign. The variant received -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MRPS12 | NM_033362.4 | c.144G>T | p.Lys48Asn | missense_variant | Exon 3 of 3 | ENST00000308018.9 | NP_203526.1 | |
MRPS12 | NM_021107.1 | c.144G>T | p.Lys48Asn | missense_variant | Exon 2 of 2 | NP_066930.1 | ||
MRPS12 | NM_033363.1 | c.144G>T | p.Lys48Asn | missense_variant | Exon 3 of 3 | NP_203527.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MRPS12 | ENST00000308018.9 | c.144G>T | p.Lys48Asn | missense_variant | Exon 3 of 3 | 1 | NM_033362.4 | ENSP00000308845.3 | ||
MRPS12 | ENST00000402029.3 | c.144G>T | p.Lys48Asn | missense_variant | Exon 3 of 3 | 1 | ENSP00000384579.2 | |||
MRPS12 | ENST00000407800.2 | c.144G>T | p.Lys48Asn | missense_variant | Exon 2 of 2 | 1 | ENSP00000384952.1 | |||
ENSG00000269547 | ENST00000599996.1 | c.475-6127C>A | intron_variant | Intron 5 of 19 | 2 | ENSP00000472465.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD2 exomes AF: 0.00000805 AC: 2AN: 248334 AF XY: 0.0000149 show subpopulations
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1458604Hom.: 0 Cov.: 31 AF XY: 0.00000552 AC XY: 4AN XY: 725186 show subpopulations
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.144G>T (p.K48N) alteration is located in exon 3 (coding exon 2) of the MRPS12 gene. This alteration results from a G to T substitution at nucleotide position 144, causing the lysine (K) at amino acid position 48 to be replaced by an asparagine (N). 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