rs37747

Positions:

• chr7-111280124-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032549.4(IMMP2L):​c.239+207114G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0843 in 152,208 control chromosomes in the GnomAD database, including 619 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 0.084 (619 hom., cov: 32)
• Consequence: IMMP2L NM_032549.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IMMP2L	NM_032549.4	c.239+207114G>C		intron_variant		ENST00000405709.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IMMP2L	ENST00000405709.7	c.239+207114G>C		intron_variant		1	NM_032549.4	P1

Frequencies

GnomAD3 genomes AF: 0.0844 AC: 12829 AN: 152090 Hom.: 621 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0561

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.0222

Gnomad FIN AF: 0.0688

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0837

Gnomad OTH AF: 0.0951

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

GnomAD4 genome AF: 0.0843 AC: 12828 AN: 152208 Hom.: 619 Cov.: 32 AF XY: 0.0802 AC XY: 5971 AN XY: 74420

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.0560

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.000775

Gnomad4 SAS AF: 0.0220

Gnomad4 FIN AF: 0.0688

Gnomad4 NFE AF: 0.0837

Gnomad4 OTH AF: 0.0937

Alfa AF: 0.0905 Hom.: 89

Bravo AF: 0.0869

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.59

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: rs37747; hg19: chr7-110920180;