chr13-23854958-C-A

Variant names:

• chr13-23854958-C-A
• rs9507174
• NM_005932.4:c.1106+3902G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005932.4(MIPEP):​c.1106+3902G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,282 control chromosomes in the GnomAD database, including 16,973 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 0.47 (16973 hom., cov: 31)
• Consequence: MIPEP NM_005932.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIPEP	NM_005932.4	c.1106+3902G>T		intron_variant	Intron 10 of 18	ENST00000382172.4	NP_005923.3
MIPEP	XM_011535097.3	c.920+3902G>T		intron_variant	Intron 10 of 18		XP_011533399.1
MIPEP	XM_011535098.4	c.1106+3902G>T		intron_variant	Intron 10 of 16		XP_011533400.1
MIPEP	XM_047430368.1	c.920+3902G>T		intron_variant	Intron 10 of 16		XP_047286324.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIPEP	ENST00000382172.4	c.1106+3902G>T		intron_variant	Intron 10 of 18	1	NM_005932.4	ENSP00000371607.3
MIPEP	ENST00000494139.1	n.503+3902G>T		intron_variant	Intron 5 of 5	2

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70616 AN: 151174 Hom.: 16968 Cov.: 31

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.467 AC: 70661 AN: 151282 Hom.: 16973 Cov.: 31 AF XY: 0.467 AC XY: 34510 AN XY: 73872

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.485

Alfa AF: 0.499 Hom.: 8315

Bravo AF: 0.453

Asia WGS AF: 0.520 AC: 1807 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.8
DANN	Benign	0.69

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

Other links and lift over

dbSNP: rs9507174; hg19: chr13-24429097;