NM_014161.5:c.152_153delGGinsTT

Variant names:

• chr6-159791039-GG-TT
• NM_014161.5:c.152_153delGGinsTT
• MRPL18 p.Arg51Leu

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_014161.5(MRPL18):​c.152_153delGGinsTT​(p.Arg51Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R51W) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MRPL18 NM_014161.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.00
• Publications: 0 publications found

Genes affected

MRPL18 (HGNC:14477): (mitochondrial ribosomal protein L18) This nuclear gene encodes a protein component of the larger 39S subunit of mitochondrial ribosome. This protein may also aid in the import of nuclear-encoded 5S rRNA into mitochondria. Alternative splicing results in multiple transcript variants, most of which are not predicted to encode a protein. A pseudogene of this gene is found on chromosome 16. [provided by RefSeq, Jan 2016]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014161.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPL18	NM_014161.5	MANE Select	c.152_153delGGinsTT	p.Arg51Leu	missense	N/A	NP_054880.2
	MRPL18	NM_001318817.2		c.152_153delGGinsTT	p.Arg51Leu	missense	N/A	NP_001305746.1
	MRPL18	NR_134860.1		n.414_415delGGinsTT		non_coding_transcript_exon	Exon 3 of 5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPL18	ENST00000367034.5	TSL:1 MANE Select	c.152_153delGGinsTT	p.Arg51Leu	missense	N/A	ENSP00000356001.4	Q9H0U6
	MRPL18	ENST00000953331.1		c.179_180delGGinsTT	p.Arg60Leu	missense	N/A	ENSP00000623390.1
	MRPL18	ENST00000857674.1		c.152_153delGGinsTT	p.Arg51Leu	missense	N/A	ENSP00000527733.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr6-160212071;