rs725272

Positions:

• chr7-110946071-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032549.4(IMMP2L):​c.305+17429C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 151,988 control chromosomes in the GnomAD database, including 17,682 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.46 (17682 hom., cov: 32)
• Consequence: IMMP2L NM_032549.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480

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]

IMMP2L (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IMMP2L	NM_032549.4	c.305+17429C>G		intron_variant		ENST00000405709.7	NP_115938.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IMMP2L	ENST00000405709.7	c.305+17429C>G		intron_variant		1	NM_032549.4	ENSP00000384966.2

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69611 AN: 151870 Hom.: 17681 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.458 AC: 69621 AN: 151988 Hom.: 17682 Cov.: 32 AF XY: 0.454 AC XY: 33725 AN XY: 74280

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.465

Alfa AF: 0.522 Hom.: 2716

Bravo AF: 0.449

Asia WGS AF: 0.196 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.63

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: rs725272; hg19: chr7-110586127;