11-31485360-T-G

Variant names:

• chr11-31485360-T-G
• rs1223098
• NM_001304274.2:c.-29-22055A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001304274.2(IMMP1L):​c.-29-22055A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 151,620 control chromosomes in the GnomAD database, including 33,454 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 0.65 (33454 hom., cov: 32)
• Consequence: IMMP1L NM_001304274.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 4 publications found

Genes affected

IMMP1L (HGNC:26317): (inner mitochondrial membrane peptidase subunit 1) The mitochondrial inner membrane peptidase (IMP) complex generates mature, active proteins in the mitochondrial intermembrane space by proteolytically removing the mitochondrial targeting presequence of nuclear-encoded proteins. IMP1 and IMP2 (IMMP2L; MIM 605977) are the catalytic subunits of the IMP complex (Burri et al., 2005 [PubMed 15814844]).[supplied by OMIM, Sep 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304274.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IMMP1L	NM_001304274.2	MANE Select	c.-29-22055A>C		intron	N/A	NP_001291203.1
	IMMP1L	NM_144981.3		c.-92-11574A>C		intron	N/A	NP_659418.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IMMP1L	ENST00000532287.6	TSL:1 MANE Select	c.-29-22055A>C		intron	N/A	ENSP00000435576.1
	IMMP1L	ENST00000528161.5	TSL:1	n.45+24159A>C		intron	N/A
	IMMP1L	ENST00000532624.5	TSL:1	n.88-22055A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97696 AN: 151502 Hom.: 33388 Cov.: 32

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.645 AC: 97823 AN: 151620 Hom.: 33454 Cov.: 32 AF XY: 0.637 AC XY: 47185 AN XY: 74108

African (AFR) AF: 0.886 AC: 36749 AN: 41496

American (AMR) AF: 0.647 AC: 9836 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2152 AN: 3458

East Asian (EAS) AF: 0.372 AC: 1922 AN: 5160

South Asian (SAS) AF: 0.548 AC: 2640 AN: 4814

European-Finnish (FIN) AF: 0.443 AC: 4677 AN: 10552

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37627 AN: 67634

Other (OTH) AF: 0.648 AC: 1357 AN: 2094

Alfa AF: 0.436 Hom.: 1080

Bravo AF: 0.670

Asia WGS AF: 0.517 AC: 1798 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.36
PhyloP100		-1.9
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: rs1223098; hg19: chr11-31506907;