rs725272

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000405709.7(IMMP2L):​c.305+17429C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 151,988 control chromosomes in the GnomAD database, including 17,682 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 0.46 ( 17682 hom., cov: 32)

Consequence

IMMP2L
ENST00000405709.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.480
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IMMP2LNM_032549.4 linkuse as main transcriptc.305+17429C>G intron_variant ENST00000405709.7 NP_115938.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IMMP2LENST00000405709.7 linkuse as main transcriptc.305+17429C>G intron_variant 1 NM_032549.4 ENSP00000384966 P1Q96T52-1

Frequencies

GnomAD3 genomes
AF:
0.458
AC:
69611
AN:
151870
Hom.:
17681
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.267
Gnomad AMI
AF:
0.663
Gnomad AMR
AF:
0.496
Gnomad ASJ
AF:
0.546
Gnomad EAS
AF:
0.151
Gnomad SAS
AF:
0.275
Gnomad FIN
AF:
0.538
Gnomad MID
AF:
0.490
Gnomad NFE
AF:
0.582
Gnomad OTH
AF:
0.472
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.458
AC:
69621
AN:
151988
Hom.:
17682
Cov.:
32
AF XY:
0.454
AC XY:
33725
AN XY:
74280
show subpopulations
Gnomad4 AFR
AF:
0.267
Gnomad4 AMR
AF:
0.496
Gnomad4 ASJ
AF:
0.546
Gnomad4 EAS
AF:
0.151
Gnomad4 SAS
AF:
0.275
Gnomad4 FIN
AF:
0.538
Gnomad4 NFE
AF:
0.582
Gnomad4 OTH
AF:
0.465
Alfa
AF:
0.522
Hom.:
2716
Bravo
AF:
0.449
Asia WGS
AF:
0.196
AC:
687
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
1.5
DANN
Benign
0.63

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs725272; hg19: chr7-110586127; API