Variant rs16843829 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_000532.5(PCCB):c.372+31T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00601 in 1,449,700 control chromosomes in the GnomAD database, including 663 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0071 ( 75 hom., cov: 33)

Exomes 𝑓: 0.0059 ( 588 hom. )

Consequence

PCCB
NM_000532.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.121

Variant links:

Genes affected

PCCB (HGNC:8654): (propionyl-CoA carboxylase subunit beta) The protein encoded by this gene is a subunit of the propionyl-CoA carboxylase (PCC) enzyme, which is involved in the catabolism of propionyl-CoA. PCC is a mitochondrial enzyme that probably acts as a dodecamer of six alpha subunits and six beta subunits. This gene encodes the beta subunit of PCC. Defects in this gene are a cause of propionic acidemia type II (PA-2). Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2010]

PCCB links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 3-136256654-T-C is Benign according to our data. Variant chr3-136256654-T-C is described in ClinVar as [Benign]. Clinvar id is 256374.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
PCCB	NM_000532.5 linkuse as main transcript	c.372+31T>C	intron_variant	ENST00000251654.9
PCCB	NM_001178014.2 linkuse as main transcript	c.372+31T>C	intron_variant
PCCB	XM_011512873.2 linkuse as main transcript	c.372+31T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCCB	ENST00000251654.9 linkuse as main transcript	c.372+31T>C		intron_variant		1	NM_000532.5	P2	P05166-1

Frequencies

GnomAD3 genomes

AF:

0.00705

AC:

1073

AN:

152214

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00154

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00353

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.168

Gnomad SAS

AF:

0.00475

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000426

Gnomad OTH

AF:

0.00622

GnomAD3 exomes

AF:

0.0148

AC:

3725

AN:

251186

Hom.:

325

AF XY:

0.0135

AC XY:

1839

AN XY:

135772

show subpopulations

Gnomad AFR exome

AF:

0.00166

Gnomad AMR exome

AF:

0.00223

Gnomad ASJ exome

AF:

0.00328

Gnomad EAS exome

AF:

0.187

Gnomad SAS exome

AF:

0.00206

Gnomad FIN exome

AF:

0.000462

Gnomad NFE exome

AF:

0.000255

Gnomad OTH exome

AF:

0.00751

GnomAD4 exome

AF:

0.00589

AC:

7640

AN:

1297368

Hom.:

588

Cov.:

AF XY:

0.00557

AC XY:

3644

AN XY:

654008

show subpopulations

Gnomad4 AFR exome

AF:

0.000858

Gnomad4 AMR exome

AF:

0.00209

Gnomad4 ASJ exome

AF:

0.00287

Gnomad4 EAS exome

AF:

0.158

Gnomad4 SAS exome

AF:

0.00286

Gnomad4 FIN exome

AF:

0.000319

Gnomad4 NFE exome

AF:

0.000160

Gnomad4 OTH exome

AF:

0.0162

GnomAD4 genome

AF:

0.00706

AC:

1075

AN:

152332

Hom.:

Cov.:

AF XY:

0.00758

AC XY:

565

AN XY:

74494

show subpopulations

Gnomad4 AFR

AF:

0.00154

Gnomad4 AMR

AF:

0.00353

Gnomad4 ASJ

AF:

0.00317

Gnomad4 EAS

AF:

0.169

Gnomad4 SAS

AF:

0.00455

Gnomad4 FIN

AF:

0.000377

Gnomad4 NFE

AF:

0.000426

Gnomad4 OTH

AF:

0.00663

Alfa

AF:

0.00276

Hom.:

Bravo

AF:

0.00845

Asia WGS

AF:

0.0790

AC:

272

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 27, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

DANN

Benign

0.77

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