rs1569122

chr7-110819871-G-A

Variant summary

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

The NM_032549.4(IMMP2L):c.408+66722C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 133,550 control chromosomes in the GnomAD database, including 4,040 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 0.25 (4040 hom., cov: 31)
• Consequence: IMMP2L NM_032549.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.881

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IMMP2L	NM_032549.4	c.408+66722C>T		intron_variant		ENST00000405709.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IMMP2L	ENST00000405709.7	c.408+66722C>T		intron_variant		1	NM_032549.4	P1

Frequencies

GnomAD3 genomes AF: 0.247 AC: 32969 AN: 133450 Hom.: 4038 Cov.: 31

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.164

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.247 AC: 33008 AN: 133550 Hom.: 4040 Cov.: 31 AF XY: 0.249 AC XY: 16273 AN XY: 65468

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.232

Alfa AF: 0.167 Hom.: 3719

Bravo AF: 0.220

Asia WGS AF: 0.236 AC: 806 AN: 3412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.76
Dann	Benign	0.45

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: rs1569122; hg19: chr7-110459927;