chr13-23858328-A-G

Variant summary

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

The NM_005932.4(MIPEP):​c.1106+532T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,788 control chromosomes in the GnomAD database, including 23,515 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 0.55 ( 23515 hom., cov: 30)

Consequence

MIPEP
NM_005932.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0300
Variant links:
Genes affected
MIPEP (HGNC:7104): (mitochondrial intermediate peptidase) The product of this gene performs the final step in processing a specific class of nuclear-encoded proteins targeted to the mitochondrial matrix or inner membrane. This protein is primarily involved in the maturation of oxidative phosphorylation (OXPHOS)-related proteins. This gene may contribute to the functional effects of frataxin deficiency and the clinical manifestations of Friedreich ataxia. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MIPEPNM_005932.4 linkuse as main transcriptc.1106+532T>C intron_variant ENST00000382172.4
MIPEPXM_011535097.3 linkuse as main transcriptc.920+532T>C intron_variant
MIPEPXM_011535098.4 linkuse as main transcriptc.1106+532T>C intron_variant
MIPEPXM_047430368.1 linkuse as main transcriptc.920+532T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MIPEPENST00000382172.4 linkuse as main transcriptc.1106+532T>C intron_variant 1 NM_005932.4 P1
MIPEPENST00000494139.1 linkuse as main transcriptn.503+532T>C intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.554
AC:
84087
AN:
151672
Hom.:
23486
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.563
Gnomad AMI
AF:
0.457
Gnomad AMR
AF:
0.593
Gnomad ASJ
AF:
0.548
Gnomad EAS
AF:
0.541
Gnomad SAS
AF:
0.722
Gnomad FIN
AF:
0.497
Gnomad MID
AF:
0.544
Gnomad NFE
AF:
0.540
Gnomad OTH
AF:
0.550
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.555
AC:
84168
AN:
151788
Hom.:
23515
Cov.:
30
AF XY:
0.555
AC XY:
41204
AN XY:
74182
show subpopulations
Gnomad4 AFR
AF:
0.563
Gnomad4 AMR
AF:
0.594
Gnomad4 ASJ
AF:
0.548
Gnomad4 EAS
AF:
0.543
Gnomad4 SAS
AF:
0.721
Gnomad4 FIN
AF:
0.497
Gnomad4 NFE
AF:
0.540
Gnomad4 OTH
AF:
0.555
Alfa
AF:
0.544
Hom.:
49811
Bravo
AF:
0.556
Asia WGS
AF:
0.659
AC:
2293
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.92
DANN
Benign
0.65

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: rs9318086; hg19: chr13-24432467; API