11-31458802-T-G

Variant names:

• chr11-31458802-T-G
• rs1223068
• NM_001304274.2:c.194+1824A>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.194+1824A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,114 control chromosomes in the GnomAD database, including 12,151 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 (12151 hom., cov: 32)
• Consequence: IMMP1L NM_001304274.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IMMP1L	NM_001304274.2	c.194+1824A>C		intron_variant	Intron 3 of 5	ENST00000532287.6	NP_001291203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IMMP1L	ENST00000532287.6	c.194+1824A>C		intron_variant	Intron 3 of 5	1	NM_001304274.2	ENSP00000435576.1

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54818 AN: 151996 Hom.: 12107 Cov.: 32

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.361 AC: 54925 AN: 152114 Hom.: 12151 Cov.: 32 AF XY: 0.356 AC XY: 26484 AN XY: 74354

African (AFR) AF: 0.626 AC: 25955 AN: 41482

American (AMR) AF: 0.377 AC: 5753 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1071 AN: 3470

East Asian (EAS) AF: 0.319 AC: 1647 AN: 5166

South Asian (SAS) AF: 0.341 AC: 1641 AN: 4812

European-Finnish (FIN) AF: 0.141 AC: 1490 AN: 10604

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16293 AN: 67986

Other (OTH) AF: 0.374 AC: 790 AN: 2110

Alfa AF: 0.387 Hom.: 3037

Bravo AF: 0.390

Asia WGS AF: 0.383 AC: 1332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.32
DANN	Benign	0.38
PhyloP100		-0.93
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1223068; hg19: chr11-31480349;