rs868824

Positions:

• chr7-110751865-T-C
• chr7-110751865-T-G

Variant summary

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

The NM_032549.4(IMMP2L):​c.409-88144A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 151,914 control chromosomes in the GnomAD database, including 10,204 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 0.33 (10204 hom., cov: 32)
• Consequence: IMMP2L NM_032549.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IMMP2L	NM_032549.4	c.409-88144A>G		intron_variant		ENST00000405709.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IMMP2L	ENST00000405709.7	c.409-88144A>G		intron_variant		1	NM_032549.4	P1

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50205 AN: 151796 Hom.: 10201 Cov.: 32

Gnomad AFR AF: 0.0858

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.331 AC: 50211 AN: 151914 Hom.: 10204 Cov.: 32 AF XY: 0.336 AC XY: 24953 AN XY: 74248

Gnomad4 AFR AF: 0.0856

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.328

Alfa AF: 0.371 Hom.: 4937

Bravo AF: 0.319

Asia WGS AF: 0.456 AC: 1582 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	13
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: rs868824; hg19: chr7-110391921;