rs37648

Positions:

• chr7-111343948-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.239+143290G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,806 control chromosomes in the GnomAD database, including 24,558 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 0.56 (24558 hom., cov: 31)
• Consequence: IMMP2L NM_032549.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174

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]

LOC124900232 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IMMP2L	NM_032549.4	c.239+143290G>A		intron_variant		ENST00000405709.7
LOC124900232	XR_007060475.1	n.45443G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IMMP2L	ENST00000405709.7	c.239+143290G>A		intron_variant		1	NM_032549.4	P1

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84936 AN: 151690 Hom.: 24505 Cov.: 31

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.560 AC: 85053 AN: 151806 Hom.: 24558 Cov.: 31 AF XY: 0.562 AC XY: 41732 AN XY: 74194

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.588

Alfa AF: 0.512 Hom.: 3406

Bravo AF: 0.571

Asia WGS AF: 0.682 AC: 2370 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
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: rs37648; hg19: chr7-110984004;