Variant 13-23760076-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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:3

Conservation

PhyloP100: 0.497

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MIPEP	NM_005932.4 linkuse as main transcript	c.1970+20A>C		intron_variant		ENST00000382172.4
MIPEP	XM_011535097.3 linkuse as main transcript	c.1784+20A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIPEP	ENST00000382172.4 linkuse as main transcript	c.1970+20A>C		intron_variant		1	NM_005932.4	P1
MIPEP	ENST00000433710.2 linkuse as main transcript	n.163+20A>C		intron_variant, non_coding_transcript_variant		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

GnomAD3 exomes

AF:

0.201

AC:

50414

AN:

251136

Hom.:

6075

AF XY:

0.208

AC XY:

28174

AN XY:

135712

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 SAS exome

AF:

0.168

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

Gnomad4 AFR exome

AF:

0.0980

Gnomad4 AMR exome

AF:

0.117

Gnomad4 ASJ exome

AF:

0.219

Gnomad4 EAS exome

AF:

0.000731

Gnomad4 SAS exome

AF:

0.171

Gnomad4 FIN exome

AF:

0.204

Gnomad4 NFE exome

AF:

0.290

Gnomad4 OTH exome

AF:

0.233

GnomAD4 genome

AF:

0.203

AC:

30888

AN:

152038

Hom.:

3814

Cov.:

AF XY:

0.200

AC XY:

14837

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.106

Gnomad4 AMR

AF:

0.174

Gnomad4 ASJ

AF:

0.219

Gnomad4 EAS

AF:

0.000581

Gnomad4 SAS

AF:

0.173

Gnomad4 FIN

AF:

0.204

Gnomad4 NFE

AF:

0.283

Gnomad4 OTH

AF:

0.207

Alfa

AF:

0.240

Hom.:

1055

Bravo

AF:

0.194

Asia WGS

AF:

0.0740

AC:

258

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 30, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 13, 2021	- -

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

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

Cadd

Benign

3.3

Dann

Benign

0.47

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

LitVar

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over