Variant 7-103297437-C-T 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_004279.3(PMPCB):c.-23C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00762 in 1,533,296 control chromosomes in the GnomAD database, including 678 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.010 ( 67 hom., cov: 33)

Exomes 𝑓: 0.0073 ( 611 hom. )

Consequence

PMPCB
NM_004279.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.897

Variant links:

Genes affected

PMPCB (HGNC:9119): (peptidase, mitochondrial processing subunit beta) This gene is a member of the peptidase M16 family and encodes a protein with a zinc-binding motif. This protein is located in the mitochondrial matrix and catalyzes the cleavage of the leader peptides of precursor proteins newly imported into the mitochondria, though it only functions as part of a heterodimeric complex. [provided by RefSeq, Jul 2008]

PMPCB 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=-0.88).

BP6

Variant 7-103297437-C-T is Benign according to our data. Variant chr7-103297437-C-T is described in ClinVar as [Benign]. Clinvar id is 1179481.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PMPCB	NM_004279.3 linkuse as main transcript	c.-23C>T		5_prime_UTR_variant	1/13	ENST00000249269.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PMPCB	ENST00000249269.9 linkuse as main transcript	c.-23C>T		5_prime_UTR_variant	1/13	1	NM_004279.3	P1

Frequencies

GnomAD3 genomes

AF:

0.0101

AC:

1534

AN:

152190

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00106

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00157

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.136

Gnomad SAS

AF:

0.00745

Gnomad FIN

AF:

0.0586

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00126

Gnomad OTH

AF:

0.00669

GnomAD3 exomes

AF:

0.0181

AC:

3486

AN:

192074

Hom.:

211

AF XY:

0.0178

AC XY:

1810

AN XY:

101580

show subpopulations

Gnomad AFR exome

AF:

0.000852

Gnomad AMR exome

AF:

0.000355

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.134

Gnomad SAS exome

AF:

0.00394

Gnomad FIN exome

AF:

0.0549

Gnomad NFE exome

AF:

0.00201

Gnomad OTH exome

AF:

0.0110

GnomAD4 exome

AF:

0.00735

AC:

10149

AN:

1380988

Hom.:

611

Cov.:

AF XY:

0.00731

AC XY:

4954

AN XY:

677676

show subpopulations

Gnomad4 AFR exome

AF:

0.000582

Gnomad4 AMR exome

AF:

0.000293

Gnomad4 ASJ exome

AF:

0.0000958

Gnomad4 EAS exome

AF:

0.159

Gnomad4 SAS exome

AF:

0.00414

Gnomad4 FIN exome

AF:

0.0510

Gnomad4 NFE exome

AF:

0.000602

Gnomad4 OTH exome

AF:

0.00823

GnomAD4 genome

AF:

0.0101

AC:

1537

AN:

152308

Hom.:

Cov.:

AF XY:

0.0134

AC XY:

998

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.00106

Gnomad4 AMR

AF:

0.00157

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.137

Gnomad4 SAS

AF:

0.00725

Gnomad4 FIN

AF:

0.0586

Gnomad4 NFE

AF:

0.00126

Gnomad4 OTH

AF:

0.00804

Alfa

AF:

0.00216

Hom.:

Bravo

AF:

0.00626

Asia WGS

AF:

0.0500

AC:

172

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 21, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

9.0

DANN

Benign

0.79

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.

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