rs17157913

Variant names:

• chr7-110700918-T-C
• rs17157913
• NM_032549.4:c.409-37197A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032549.4(IMMP2L):​c.409-37197A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0536 in 152,302 control chromosomes in the GnomAD database, including 295 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 0.054 (295 hom., cov: 33)
• Consequence: IMMP2L NM_032549.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422
• Publications: 3 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IMMP2L	NM_032549.4	MANE Select	c.409-37197A>G		intron	N/A	NP_115938.1	Q96T52-1
	IMMP2L	NM_001350961.2		c.493-37197A>G		intron	N/A	NP_001337890.1
	IMMP2L	NM_001244606.2		c.409-37197A>G		intron	N/A	NP_001231535.1	Q96T52-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IMMP2L	ENST00000405709.7	TSL:1 MANE Select	c.409-37197A>G		intron	N/A	ENSP00000384966.2	Q96T52-1
	IMMP2L	ENST00000331762.7	TSL:1	c.409-37197A>G		intron	N/A	ENSP00000329553.3	Q96T52-1
	IMMP2L	ENST00000452895.5	TSL:5	c.409-37197A>G		intron	N/A	ENSP00000399353.1	Q96T52-1

Frequencies

GnomAD3 genomes AF: 0.0536 AC: 8159 AN: 152184 Hom.: 297 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0310

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.00849

Gnomad FIN AF: 0.0370

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0349

Gnomad OTH AF: 0.0599

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

GnomAD4 genome AF: 0.0536 AC: 8165 AN: 152302 Hom.: 295 Cov.: 33 AF XY: 0.0531 AC XY: 3955 AN XY: 74476

African (AFR) AF: 0.108 AC: 4483 AN: 41562

American (AMR) AF: 0.0310 AC: 474 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3472

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5196

South Asian (SAS) AF: 0.00850 AC: 41 AN: 4824

European-Finnish (FIN) AF: 0.0370 AC: 393 AN: 10612

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0350 AC: 2378 AN: 68020

Other (OTH) AF: 0.0592 AC: 125 AN: 2110

Alfa AF: 0.0453 Hom.: 135

Bravo AF: 0.0560

Asia WGS AF: 0.00924 AC: 33 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.6
DANN	Benign	0.69
PhyloP100		0.42
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: rs17157913; hg19: chr7-110340974;