7-110662639-T-C

Variant names:

• chr7-110662639-T-C
• rs1525677
• NM_032549.4:c.*963A>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.*963A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,072 control chromosomes in the GnomAD database, including 10,493 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 0.36 (10493 hom., cov: 33)
• Consequence: IMMP2L NM_032549.4 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 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.*963A>G		downstream_gene	N/A	NP_115938.1	Q96T52-1
	IMMP2L	NM_001350961.2		c.*963A>G		downstream_gene	N/A	NP_001337890.1
	IMMP2L	NM_001244606.2		c.*963A>G		downstream_gene	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.*963A>G		downstream_gene	N/A	ENSP00000384966.2	Q96T52-1

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54333 AN: 151954 Hom.: 10497 Cov.: 33

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.358 AC: 54369 AN: 152072 Hom.: 10493 Cov.: 33 AF XY: 0.347 AC XY: 25823 AN XY: 74328

African (AFR) AF: 0.501 AC: 20771 AN: 41460

American (AMR) AF: 0.272 AC: 4163 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1061 AN: 3468

East Asian (EAS) AF: 0.133 AC: 689 AN: 5172

South Asian (SAS) AF: 0.175 AC: 845 AN: 4826

European-Finnish (FIN) AF: 0.273 AC: 2878 AN: 10544

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22805 AN: 67978

Other (OTH) AF: 0.351 AC: 742 AN: 2114

Alfa AF: 0.315 Hom.: 6299

Bravo AF: 0.367

Asia WGS AF: 0.163 AC: 568 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.010
DANN	Benign	0.46
PhyloP100		-2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1525677; hg19: chr7-110302695;