7-110886666-TT-CG

Variant names:

• chr7-110886666-TT-CG
• NM_032549.4:c.334_335delAAinsCG
• IMMP2L p.Lys112Arg

Variant summary

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

The NM_032549.4(IMMP2L):​c.334_335delAAinsCG​(p.Lys112Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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 Benign in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: IMMP2L NM_032549.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.11
• Publications: 0 publications found

Genes affected

IMMP2L (HGNC:14598): (inner mitochondrial membrane peptidase subunit 2) This gene encodes a protein involved in processing the signal peptide sequences used to direct mitochondrial proteins to the mitochondria. The encoded protein resides in the mitochondria and is one of the necessary proteins for the catalytic activity of the mitochondrial inner membrane peptidase (IMP) complex. Two variants that encode the same protein have been described for this gene. [provided by RefSeq, Sep 2011]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032549.4. 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
	IMMP2L	NM_032549.4	MANE Select	c.334_335delAAinsCG	p.Lys112Arg	missense	N/A	NP_115938.1	Q96T52-1
	IMMP2L	NM_001350961.2		c.418_419delAAinsCG	p.Lys140Arg	missense	N/A	NP_001337890.1
	IMMP2L	NM_001244606.2		c.334_335delAAinsCG	p.Lys112Arg	missense	N/A	NP_001231535.1	Q96T52-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IMMP2L	ENST00000405709.7	TSL:1 MANE Select	c.334_335delAAinsCG	p.Lys112Arg	missense	N/A	ENSP00000384966.2	Q96T52-1
	IMMP2L	ENST00000331762.7	TSL:1	c.334_335delAAinsCG	p.Lys112Arg	missense	N/A	ENSP00000329553.3	Q96T52-1
	IMMP2L	ENST00000452895.5	TSL:5	c.334_335delAAinsCG	p.Lys112Arg	missense	N/A	ENSP00000399353.1	Q96T52-1

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		3.1

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: chr7-110526722;