rs10500002

Positions:

• chr7-110801799-G-A

Variant summary

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

The ENST00000405709.7(IMMP2L):​c.408+84794C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 151,990 control chromosomes in the GnomAD database, including 1,936 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 0.15 (1936 hom., cov: 32)
• Consequence: IMMP2L ENST00000405709.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.868

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IMMP2L	NM_032549.4	c.408+84794C>T		intron_variant		ENST00000405709.7	NP_115938.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IMMP2L	ENST00000405709.7	c.408+84794C>T		intron_variant		1	NM_032549.4	ENSP00000384966	P1

Frequencies

GnomAD3 genomes AF: 0.151 AC: 23007 AN: 151872 Hom.: 1939 Cov.: 32

Gnomad AFR AF: 0.0967

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.151 AC: 23008 AN: 151990 Hom.: 1936 Cov.: 32 AF XY: 0.156 AC XY: 11610 AN XY: 74274

Gnomad4 AFR AF: 0.0966

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.156

Alfa AF: 0.162 Hom.: 2925

Bravo AF: 0.145

Asia WGS AF: 0.209 AC: 728 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.7
DANN	Benign	0.43

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: rs10500002; hg19: chr7-110441855;