NM_032549.4:c.239+187307_239+187310delACTT

Variant names:

• chr7-111299927-CAAGT-C
• rs1611048
• NM_032549.4:c.239+187307_239+187310delACTT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_032549.4(IMMP2L):​c.239+187307_239+187310delACTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.54 (22817 hom., cov: 0)
• Consequence: IMMP2L NM_032549.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.405
• Publications: 4 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: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

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.239+187307_239+187310delACTT		intron	N/A	NP_115938.1	Q96T52-1
	IMMP2L	NM_001350961.2		c.323+117328_323+117331delACTT		intron	N/A	NP_001337890.1
	IMMP2L	NM_001244606.2		c.239+187307_239+187310delACTT		intron	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.239+187307_239+187310delACTT		intron	N/A	ENSP00000384966.2	Q96T52-1
	IMMP2L	ENST00000331762.7	TSL:1	c.239+187307_239+187310delACTT		intron	N/A	ENSP00000329553.3	Q96T52-1
	IMMP2L	ENST00000452895.5	TSL:5	c.239+187307_239+187310delACTT		intron	N/A	ENSP00000399353.1	Q96T52-1

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82245 AN: 151366 Hom.: 22773 Cov.: 0

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.544 AC: 82356 AN: 151484 Hom.: 22817 Cov.: 0 AF XY: 0.546 AC XY: 40377 AN XY: 73982

African (AFR) AF: 0.632 AC: 26096 AN: 41294

American (AMR) AF: 0.585 AC: 8902 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2135 AN: 3460

East Asian (EAS) AF: 0.548 AC: 2818 AN: 5146

South Asian (SAS) AF: 0.706 AC: 3399 AN: 4812

European-Finnish (FIN) AF: 0.458 AC: 4800 AN: 10476

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.479 AC: 32499 AN: 67782

Other (OTH) AF: 0.578 AC: 1209 AN: 2090

Alfa AF: 0.510 Hom.: 2468

Bravo AF: 0.554

Asia WGS AF: 0.683 AC: 2375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.41
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

dbSNP: rs1611048; hg19: chr7-110939983;