rs3795270

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002617.4(PEX10):c.*11G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.028 in 1,594,616 control chromosomes in the GnomAD database, including 908 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.035 ( 144 hom., cov: 34)

Exomes 𝑓: 0.027 ( 764 hom. )

Consequence

PEX10
NM_002617.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -1.68

Publications

3 publications found

Variant links:

Genes affected

PEX10 (HGNC:8851): (peroxisomal biogenesis factor 10) This gene encodes a protein involved in import of peroxisomal matrix proteins. This protein localizes to the peroxisomal membrane. Mutations in this gene result in phenotypes within the Zellweger spectrum of peroxisomal biogenesis disorders, ranging from neonatal adrenoleukodystrophy to Zellweger syndrome. Alternative splicing results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

PEX10 Gene-Disease associations (from GenCC):

peroxisome biogenesis disorder
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
peroxisome biogenesis disorder 6A (Zellweger)
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Myriad Women’s Health, Ambry Genetics, G2P
peroxisome biogenesis disorder 6B
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
autosomal recessive ataxia due to PEX10 deficiency
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Zellweger spectrum disorders
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

PEX10 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 1-2405755-C-T is Benign according to our data. Variant chr1-2405755-C-T is described in ClinVar as Benign. ClinVar VariationId is 262787.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002617.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PEX10	NM_002617.4	MANE Select	c.*11G>A	3_prime_UTR	Exon 6 of 6	NP_002608.1	O60683-1
PEX10	NM_153818.2		c.*11G>A	3_prime_UTR	Exon 6 of 6	NP_722540.1	O60683-2
PEX10	NM_001374425.1		c.*11G>A	3_prime_UTR	Exon 6 of 6	NP_001361354.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PEX10	ENST00000447513.7	TSL:1 MANE Select	c.*11G>A	3_prime_UTR	Exon 6 of 6	ENSP00000407922.2	O60683-1
PEX10	ENST00000288774.8	TSL:1	c.*11G>A	3_prime_UTR	Exon 6 of 6	ENSP00000288774.3	O60683-2
PEX10	ENST00000874692.1		c.*11G>A	3_prime_UTR	Exon 6 of 6	ENSP00000544751.1

Frequencies

GnomAD3 genomes

AF:

0.0354

AC:

5383

AN:

152238

Hom.:

143

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0671

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0244

Gnomad ASJ

AF:

0.0132

Gnomad EAS

AF:

0.0327

Gnomad SAS

AF:

0.0786

Gnomad FIN

AF:

0.00527

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0220

Gnomad OTH

AF:

0.0296

GnomAD2 exomes

AF:

0.0281

AC:

6070

AN:

216298

AF XY:

0.0302

show subpopulations

Gnomad AFR exome

AF:

0.0604

Gnomad AMR exome

AF:

0.0108

Gnomad ASJ exome

AF:

0.0157

Gnomad EAS exome

AF:

0.0249

Gnomad FIN exome

AF:

0.00468

Gnomad NFE exome

AF:

0.0235

Gnomad OTH exome

AF:

0.0232

GnomAD4 exome

AF:

0.0272

AC:

39269

AN:

1442260

Hom.:

764

Cov.:

AF XY:

0.0284

AC XY:

20320

AN XY:

715756

show subpopulations

African (AFR)

AF:

0.0681

AC:

2244

AN:

32942

American (AMR)

AF:

0.0120

AC:

508

AN:

42380

Ashkenazi Jewish (ASJ)

AF:

0.0158

AC:

407

AN:

25734

East Asian (EAS)

AF:

0.0294

AC:

1132

AN:

38488

South Asian (SAS)

AF:

0.0729

AC:

6036

AN:

82848

European-Finnish (FIN)

AF:

0.00652

AC:

336

AN:

51520

Middle Eastern (MID)

AF:

0.0211

AC:

121

AN:

5740

European-Non Finnish (NFE)

AF:

0.0243

AC:

26834

AN:

1103024

Other (OTH)

AF:

0.0277

AC:

1651

AN:

59584

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

1966

3931

5897

7862

9828

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1074

2148

3222

4296

5370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0354

AC:

5395

AN:

152356

Hom.:

144

Cov.:

AF XY:

0.0350

AC XY:

2607

AN XY:

74522

show subpopulations

African (AFR)

AF:

0.0674

AC:

2801

AN:

41566

American (AMR)

AF:

0.0244

AC:

373

AN:

15312

Ashkenazi Jewish (ASJ)

AF:

0.0132

AC:

AN:

3472

East Asian (EAS)

AF:

0.0330

AC:

171

AN:

5182

South Asian (SAS)

AF:

0.0774

AC:

374

AN:

4832

European-Finnish (FIN)

AF:

0.00527

AC:

AN:

10628

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0220

AC:

1497

AN:

68042

Other (OTH)

AF:

0.0288

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

267

534

801

1068

1335

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

192

256

320

<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:

0.0237

Hom.:

Bravo

AF:

0.0357

Asia WGS

AF:

0.0500

AC:

174

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

not specified (2)

Peroxisome biogenesis disorder 6A (Zellweger) (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.70

(source)

DANN

Benign

0.75

PhyloP100

-1.7

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over