rs37655

Positions:

• chr7-111355009-G-A

Variant summary

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

The NM_032549.4(IMMP2L):​c.239+132229C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.054 in 151,806 control chromosomes in the GnomAD database, including 323 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 (323 hom., cov: 32)
• Consequence: IMMP2L NM_032549.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IMMP2L	NM_032549.4	c.239+132229C>T		intron_variant		ENST00000405709.7
LOC124900232	XR_007060475.1	n.34382C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IMMP2L	ENST00000405709.7	c.239+132229C>T		intron_variant		1	NM_032549.4	P1

Frequencies

GnomAD3 genomes AF: 0.0540 AC: 8197 AN: 151688 Hom.: 325 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0336

Gnomad ASJ AF: 0.0534

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0129

Gnomad FIN AF: 0.0258

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0396

Gnomad OTH AF: 0.0582

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

GnomAD4 genome AF: 0.0540 AC: 8195 AN: 151806 Hom.: 323 Cov.: 32 AF XY: 0.0507 AC XY: 3760 AN XY: 74192

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.0335

Gnomad4 ASJ AF: 0.0534

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0125

Gnomad4 FIN AF: 0.0258

Gnomad4 NFE AF: 0.0396

Gnomad4 OTH AF: 0.0576

Alfa AF: 0.0496 Hom.: 47

Bravo AF: 0.0581

Asia WGS AF: 0.00957 AC: 33 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.4
DANN	Benign	0.82

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: rs37655; hg19: chr7-110995065;