7-111239195-T-C

Variant names:

• chr7-111239195-T-C
• rs37715
• NM_032549.4:c.239+248043A>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.239+248043A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,632 control chromosomes in the GnomAD database, including 15,354 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 0.44 (15354 hom., cov: 31)
• Consequence: IMMP2L NM_032549.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 11 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]

LOC124901725 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IMMP2L	NM_032549.4	c.239+248043A>G		intron_variant	Intron 3 of 5	ENST00000405709.7	NP_115938.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IMMP2L	ENST00000405709.7	c.239+248043A>G		intron_variant	Intron 3 of 5	1	NM_032549.4	ENSP00000384966.2

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66622 AN: 151514 Hom.: 15360 Cov.: 31

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.439 AC: 66620 AN: 151632 Hom.: 15354 Cov.: 31 AF XY: 0.437 AC XY: 32376 AN XY: 74126

African (AFR) AF: 0.313 AC: 12989 AN: 41440

American (AMR) AF: 0.415 AC: 6320 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1339 AN: 3460

East Asian (EAS) AF: 0.403 AC: 2075 AN: 5144

South Asian (SAS) AF: 0.287 AC: 1380 AN: 4816

European-Finnish (FIN) AF: 0.534 AC: 5626 AN: 10530

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.522 AC: 35318 AN: 67708

Other (OTH) AF: 0.410 AC: 865 AN: 2110

Alfa AF: 0.494 Hom.: 44915

Bravo AF: 0.429

Asia WGS AF: 0.281 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.2
DANN	Benign	0.61
PhyloP100		0.13
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: rs37715; hg19: chr7-110879251;