13-23760076-T-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005932.4(MIPEP):c.1970+20A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 1,613,020 control chromosomes in the GnomAD database, including 56,181 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 3814 hom., cov: 32)

Exomes 𝑓: 0.26 ( 52367 hom. )

Consequence

MIPEP
NM_005932.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.497

Publications

6 publications found

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]

MIPEP Gene-Disease associations (from GenCC):

lethal left ventricular non-compaction-seizures-hypotonia-cataract-developmental delay syndrome
Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Broad Center for Mendelian Genomics
mitochondrial disease
Inheritance: AR Classification: MODERATE Submitted by: ClinGen

MIPEP links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 13-23760076-T-G is Benign according to our data. Variant chr13-23760076-T-G is described in ClinVar as [Benign]. Clinvar id is 1259605.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIPEP	NM_005932.4 link	c.1970+20A>C		intron_variant	Intron 17 of 18	ENST00000382172.4	NP_005923.3	Q99797
MIPEP	XM_011535097.3 link	c.1784+20A>C		intron_variant	Intron 17 of 18		XP_011533399.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIPEP	ENST00000382172.4 link	c.1970+20A>C		intron_variant	Intron 17 of 18	1	NM_005932.4	ENSP00000371607.3		Q99797
MIPEP	ENST00000433710.2 link	n.163+20A>C		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.203

AC:

30904

AN:

151920

Hom.:

3816

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.367

Gnomad AMR

AF:

0.174

Gnomad ASJ

AF:

0.219

Gnomad EAS

AF:

0.000580

Gnomad SAS

AF:

0.174

Gnomad FIN

AF:

0.204

Gnomad MID

AF:

0.287

Gnomad NFE

AF:

0.283

Gnomad OTH

AF:

0.210

GnomAD2 exomes

AF:

0.201

AC:

50414

AN:

251136

AF XY:

0.208

show subpopulations

Gnomad AFR exome

AF:

0.0976

Gnomad AMR exome

AF:

0.109

Gnomad ASJ exome

AF:

0.221

Gnomad EAS exome

AF:

0.000708

Gnomad FIN exome

AF:

0.204

Gnomad NFE exome

AF:

0.281

Gnomad OTH exome

AF:

0.213

GnomAD4 exome

AF:

0.258

AC:

377565

AN:

1460982

Hom.:

52367

Cov.:

AF XY:

0.257

AC XY:

186513

AN XY:

726838

show subpopulations

African (AFR)

AF:

0.0980

AC:

3279

AN:

33464

American (AMR)

AF:

0.117

AC:

5217

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.219

AC:

5727

AN:

26122

East Asian (EAS)

AF:

0.000731

AC:

AN:

39686

South Asian (SAS)

AF:

0.171

AC:

14738

AN:

86240

European-Finnish (FIN)

AF:

0.204

AC:

10909

AN:

53390

Middle Eastern (MID)

AF:

0.254

AC:

1461

AN:

5762

European-Non Finnish (NFE)

AF:

0.290

AC:

322129

AN:

1111252

Other (OTH)

AF:

0.233

AC:

14076

AN:

60342

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

13248

26497

39745

52994

66242

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.203

AC:

30888

AN:

152038

Hom.:

3814

Cov.:

AF XY:

0.200

AC XY:

14837

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.106

AC:

4377

AN:

41478

American (AMR)

AF:

0.174

AC:

2653

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.219

AC:

759

AN:

3470

East Asian (EAS)

AF:

0.000581

AC:

AN:

5162

South Asian (SAS)

AF:

0.173

AC:

836

AN:

4822

European-Finnish (FIN)

AF:

0.204

AC:

2159

AN:

10572

Middle Eastern (MID)

AF:

0.277

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.283

AC:

19249

AN:

67950

Other (OTH)

AF:

0.207

AC:

437

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1225

2450

3674

4899

6124

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.242

Hom.:

1767

Bravo

AF:

0.194

Asia WGS

AF:

0.0740

AC:

258

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

May 13, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Lethal left ventricular non-compaction-seizures-hypotonia-cataract-developmental delay syndrome

Benign:1

Sep 05, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

3.3

(source)

DANN

Benign

0.47

PhyloP100

0.50

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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13-23760076-T-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over