11-31485360-T-G

Position:

• chr11-31485360-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IMMP1L	NM_001304274.2	c.-29-22055A>C		intron_variant		ENST00000532287.6	NP_001291203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IMMP1L	ENST00000532287.6	c.-29-22055A>C		intron_variant		1	NM_001304274.2	ENSP00000435576	P1

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

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.648

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.36

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: rs1223098; hg19: chr11-31506907;