rs17157913

Positions:

• chr7-110700918-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IMMP2L	NM_032549.4	c.409-37197A>G		intron_variant		ENST00000405709.7	NP_115938.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IMMP2L	ENST00000405709.7	c.409-37197A>G		intron_variant		1	NM_032549.4	ENSP00000384966	P1

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

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0310

Gnomad4 ASJ AF: 0.0732

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.00850

Gnomad4 FIN AF: 0.0370

Gnomad4 NFE AF: 0.0350

Gnomad4 OTH AF: 0.0592

Alfa AF: 0.0474 Hom.: 87

Bravo AF: 0.0560

Asia WGS AF: 0.00924 AC: 33 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.6
DANN	Benign	0.69

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: rs17157913; hg19: chr7-110340974;