rs4730470

Positions:

• chr7-110968081-G-A
• chr7-110968081-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.240-4516C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 151,698 control chromosomes in the GnomAD database, including 32,466 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 0.65 (32466 hom., cov: 30)
• Consequence: IMMP2L NM_032549.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IMMP2L	NM_032549.4	c.240-4516C>T		intron_variant		ENST00000405709.7	NP_115938.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IMMP2L	ENST00000405709.7	c.240-4516C>T		intron_variant		1	NM_032549.4	ENSP00000384966.2

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97790 AN: 151580 Hom.: 32437 Cov.: 30

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.645 AC: 97862 AN: 151698 Hom.: 32466 Cov.: 30 AF XY: 0.637 AC XY: 47185 AN XY: 74062

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.619

Alfa AF: 0.652 Hom.: 5499

Bravo AF: 0.657

Asia WGS AF: 0.370 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.019
DANN	Benign	0.23

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: rs4730470; hg19: chr7-110608137;