Genetic Variant PEX11A:c.*865A>G (chr15-89682512-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003847.3(PEX11A):c.*865A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0747 in 152,272 control chromosomes in the GnomAD database, including 563 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 0.075 ( 563 hom., cov: 32)

Exomes 𝑓: 0.077 ( 0 hom. )

Consequence

PEX11A
NM_003847.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.527

Publications

8 publications found

Variant links:

Genes affected

PEX11A (HGNC:8852): (peroxisomal biogenesis factor 11 alpha) This gene is a member of the PEX11 family, which is composed of membrane elongation factors involved in regulation of peroxisome maintenance and proliferation. This gene product interacts with peroxisomal membrane protein 19 and may respond to outside stimuli to increase peroxisome abundance. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2012]

PEX11A Gene-Disease associations (from GenCC):

peroxisome biogenesis disorder
Inheritance: AR Classification: NO_KNOWN Submitted by: ClinGen

PEX11A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PEX11A	NM_003847.3 link	c.*865A>G	3_prime_UTR_variant	Exon 3 of 3	ENST00000300056.8	NP_003838.1	O75192-1B2R8C6
PEX11A	NM_001271572.2 link	c.*865A>G	3_prime_UTR_variant	Exon 3 of 3		NP_001258501.1	O75192-2B2R8C6
PEX11A	NM_001271573.2 link	c.*865A>G	3_prime_UTR_variant	Exon 2 of 2		NP_001258502.1	B2R8C6B4DMF6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PEX11A	ENST00000300056.8 link	c.*865A>G	3_prime_UTR_variant	Exon 3 of 3	1	NM_003847.3	ENSP00000300056.3	O75192-1
PEX11A	ENST00000561224.5 link	c.173-972A>G	intron_variant	Intron 2 of 2	4		ENSP00000453552.1	H0YMC7
PEX11A	ENST00000557982.1 link	n.207-972A>G	intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes

AF:

0.0748

AC:

11382

AN:

152128

Hom.:

562

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0195

Gnomad AMI

AF:

0.0987

Gnomad AMR

AF:

0.0580

Gnomad ASJ

AF:

0.0637

Gnomad EAS

AF:

0.134

Gnomad SAS

AF:

0.0660

Gnomad FIN

AF:

0.0967

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.0611

GnomAD4 exome

AF:

0.0769

AC:

AN:

Hom.:

Cov.:

AF XY:

0.100

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.111

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0747

AC:

11380

AN:

152246

Hom.:

563

Cov.:

AF XY:

0.0749

AC XY:

5575

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.0194

AC:

808

AN:

41566

American (AMR)

AF:

0.0579

AC:

885

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0637

AC:

221

AN:

3470

East Asian (EAS)

AF:

0.135

AC:

698

AN:

5180

South Asian (SAS)

AF:

0.0657

AC:

317

AN:

4828

European-Finnish (FIN)

AF:

0.0967

AC:

1023

AN:

10584

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.106

AC:

7198

AN:

68016

Other (OTH)

AF:

0.0624

AC:

132

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

522

1044

1565

2087

2609

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

276

414

552

690

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0900

Hom.:

1255

Bravo

AF:

0.0699

Asia WGS

AF:

0.0870

AC:

303

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.9

(source)

DANN

Benign

0.70

PhyloP100

0.53

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over