rs1611048

Positions:

• chr7-111299927-CAAGT-C
• chr7-111299927-CAAGT-CAAGTAAGT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_032549.4(IMMP2L):​c.239+187307_239+187310del 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

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

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IMMP2L	NM_032549.4	c.239+187307_239+187310del		intron_variant		ENST00000405709.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IMMP2L	ENST00000405709.7	c.239+187307_239+187310del		intron_variant		1	NM_032549.4	P1

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

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.578

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 v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs1611048; hg19: chr7-110939983;