rs37648

Variant names:

• chr7-111343948-C-T
• rs37648
• NM_032549.4:c.239+143290G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032549.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IMMP2L	NM_032549.4	MANE Select	c.239+143290G>A		intron	N/A	NP_115938.1
	IMMP2L	NM_001350961.2		c.323+73311G>A		intron	N/A	NP_001337890.1
	IMMP2L	NM_001244606.2		c.239+143290G>A		intron	N/A	NP_001231535.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IMMP2L	ENST00000405709.7	TSL:1 MANE Select	c.239+143290G>A		intron	N/A	ENSP00000384966.2
	IMMP2L	ENST00000331762.7	TSL:1	c.239+143290G>A		intron	N/A	ENSP00000329553.3
	IMMP2L	ENST00000452895.5	TSL:5	c.239+143290G>A		intron	N/A	ENSP00000399353.1

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

African (AFR) AF: 0.690 AC: 28584 AN: 41448

American (AMR) AF: 0.585 AC: 8890 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2169 AN: 3470

East Asian (EAS) AF: 0.563 AC: 2892 AN: 5138

South Asian (SAS) AF: 0.704 AC: 3373 AN: 4790

European-Finnish (FIN) AF: 0.460 AC: 4853 AN: 10546

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32555 AN: 67904

Other (OTH) AF: 0.588 AC: 1239 AN: 2106

Alfa AF: 0.528 Hom.: 7314

Bravo AF: 0.571

Asia WGS AF: 0.682 AC: 2370 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.63
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs37648; hg19: chr7-110984004;