rs37713

Positions:

• chr7-111236264-C-A
• chr7-111236264-C-T

Variant summary

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

The NM_032549.4(IMMP2L):​c.239+250974G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 151,966 control chromosomes in the GnomAD database, including 1,099 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 0.10 (1099 hom., cov: 32)
• Consequence: IMMP2L NM_032549.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IMMP2L	NM_032549.4	c.239+250974G>T		intron_variant		ENST00000405709.7
LOC124901725	XR_007060477.1	n.7299G>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IMMP2L	ENST00000405709.7	c.239+250974G>T		intron_variant		1	NM_032549.4	P1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15694 AN: 151848 Hom.: 1099 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0630

Gnomad ASJ AF: 0.0992

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0685

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0791

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.103 AC: 15711 AN: 151966 Hom.: 1099 Cov.: 32 AF XY: 0.0992 AC XY: 7373 AN XY: 74288

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.0628

Gnomad4 ASJ AF: 0.0992

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.0200

Gnomad4 FIN AF: 0.0685

Gnomad4 NFE AF: 0.0791

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0721 Hom.: 236

Bravo AF: 0.108

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.23
DANN	Benign	0.34

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: rs37713; hg19: chr7-110876320;