rs868824

Variant names:

• chr7-110751865-T-C
• rs868824
• NM_032549.4:c.409-88144A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032549.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IMMP2L	NM_032549.4	MANE Select	c.409-88144A>G		intron	N/A	NP_115938.1	Q96T52-1
	IMMP2L	NM_001350961.2		c.493-88144A>G		intron	N/A	NP_001337890.1
	IMMP2L	NM_001244606.2		c.409-88144A>G		intron	N/A	NP_001231535.1	Q96T52-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IMMP2L	ENST00000405709.7	TSL:1 MANE Select	c.409-88144A>G		intron	N/A	ENSP00000384966.2	Q96T52-1
	IMMP2L	ENST00000331762.7	TSL:1	c.409-88144A>G		intron	N/A	ENSP00000329553.3	Q96T52-1
	IMMP2L	ENST00000452895.5	TSL:5	c.409-88144A>G		intron	N/A	ENSP00000399353.1	Q96T52-1

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

African (AFR) AF: 0.0856 AC: 3554 AN: 41518

American (AMR) AF: 0.384 AC: 5828 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1351 AN: 3466

East Asian (EAS) AF: 0.694 AC: 3582 AN: 5158

South Asian (SAS) AF: 0.408 AC: 1966 AN: 4820

European-Finnish (FIN) AF: 0.411 AC: 4334 AN: 10538

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28476 AN: 67912

Other (OTH) AF: 0.328 AC: 693 AN: 2112

Alfa AF: 0.374 Hom.: 5574

Bravo AF: 0.319

Asia WGS AF: 0.456 AC: 1582 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	13
DANN	Benign	0.69
PhyloP100		1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs868824; hg19: chr7-110391921;