rs2030781

Positions:

• chr7-110722702-C-T

Variant summary

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

The NM_032549.4(IMMP2L):​c.409-58981G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 151,888 control chromosomes in the GnomAD database, including 42,491 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 0.75 (42491 hom., cov: 30)
• Consequence: IMMP2L NM_032549.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IMMP2L	NM_032549.4	c.409-58981G>A		intron_variant		ENST00000405709.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IMMP2L	ENST00000405709.7	c.409-58981G>A		intron_variant		1	NM_032549.4	P1

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113297 AN: 151770 Hom.: 42463 Cov.: 30

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.746 AC: 113378 AN: 151888 Hom.: 42491 Cov.: 30 AF XY: 0.744 AC XY: 55208 AN XY: 74208

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.751

Gnomad4 ASJ AF: 0.743

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.780

Gnomad4 OTH AF: 0.753

Alfa AF: 0.759 Hom.: 5471

Bravo AF: 0.746

Asia WGS AF: 0.708 AC: 2461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.081
DANN	Benign	0.77

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: rs2030781; hg19: chr7-110362758;