chr1-160276914-C-T

Variant names:

Variant summary

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

The NM_002857.4(PEX19):c.*2637G>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 0.0265 in 449,832 control chromosomes in the GnomAD database, including 263 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.024 ( 63 hom., cov: 32)

Exomes 𝑓: 0.028 ( 200 hom. )

Consequence

PEX19
NM_002857.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0660

Publications

4 publications found

Variant links:

Genes affected

PEX19 (HGNC:9713): (peroxisomal biogenesis factor 19) This gene is necessary for early peroxisomal biogenesis. It acts both as a cytosolic chaperone and as an import receptor for peroxisomal membrane proteins (PMPs). Peroxins (PEXs) are proteins that are essential for the assembly of functional peroxisomes. The peroxisome biogenesis disorders (PBDs) are a group of genetically heterogeneous autosomal recessive, lethal diseases characterized by multiple defects in peroxisome function. These disorders have at least 14 complementation groups, with more than one phenotype being observed for some complementation groups. Although the clinical features of PBD patients vary, cells from all PBD patients exhibit a defect in the import of one or more classes of peroxisomal matrix proteins into the organelle. Defects in this gene are a cause of Zellweger syndrome (ZWS), as well as peroxisome biogenesis disorder complementation group 14 (PBD-CG14), which is also known as PBD-CGJ. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2010]

PEX19 links:

ENSG00000258465 (HGNC:):

ENSG00000258465 links:

DCAF8-DT (HGNC:55792): (DCAF8 divergent transcript)

DCAF8-DT 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=-0.66).

BP6

Variant 1-160276914-C-T is Benign according to our data. Variant chr1-160276914-C-T is described in ClinVar as Benign. ClinVar VariationId is 293191.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0853 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002857.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PEX19	NM_002857.4	MANE Select	c.*2637G>A	3_prime_UTR	Exon 8 of 8	NP_002848.1	A0A0S2Z497
PEX19	NM_001193644.1		c.*2645G>A	3_prime_UTR	Exon 8 of 8	NP_001180573.1	P40855
PEX19	NR_036492.2		n.3436G>A	non_coding_transcript_exon	Exon 7 of 7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PEX19	ENST00000368072.10	TSL:1 MANE Select	c.*2637G>A	3_prime_UTR	Exon 8 of 8	ENSP00000357051.5	P40855-1
ENSG00000258465	ENST00000485079.1	TSL:3	c.487+1217G>A	intron	N/A	ENSP00000450870.1	H0YJ60
PEX19	ENST00000472750.5	TSL:1	n.*3304G>A	non_coding_transcript_exon	Exon 7 of 7	ENSP00000434633.1	P40855-6

Frequencies

GnomAD3 genomes

AF:

0.0242

AC:

3675

AN:

152120

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0230

Gnomad AMI

AF:

0.0439

Gnomad AMR

AF:

0.0211

Gnomad ASJ

AF:

0.0481

Gnomad EAS

AF:

0.0921

Gnomad SAS

AF:

0.0555

Gnomad FIN

AF:

0.0322

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0153

Gnomad OTH

AF:

0.0268

GnomAD2 exomes

AF:

0.0308

AC:

3981

AN:

129128

AF XY:

0.0325

show subpopulations

Gnomad AFR exome

AF:

0.0231

Gnomad AMR exome

AF:

0.0195

Gnomad ASJ exome

AF:

0.0387

Gnomad EAS exome

AF:

0.0847

Gnomad FIN exome

AF:

0.0256

Gnomad NFE exome

AF:

0.0161

Gnomad OTH exome

AF:

0.0290

GnomAD4 exome

AF:

0.0277

AC:

8255

AN:

297594

Hom.:

200

Cov.:

AF XY:

0.0300

AC XY:

5077

AN XY:

169200

show subpopulations

African (AFR)

AF:

0.0216

AC:

181

AN:

8364

American (AMR)

AF:

0.0194

AC:

521

AN:

26908

Ashkenazi Jewish (ASJ)

AF:

0.0396

AC:

423

AN:

10694

East Asian (EAS)

AF:

0.0854

AC:

781

AN:

9140

South Asian (SAS)

AF:

0.0510

AC:

3016

AN:

59114

European-Finnish (FIN)

AF:

0.0268

AC:

330

AN:

12328

Middle Eastern (MID)

AF:

0.0369

AC:

AN:

1138

European-Non Finnish (NFE)

AF:

0.0165

AC:

2582

AN:

156052

Other (OTH)

AF:

0.0274

AC:

379

AN:

13856

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

453

906

1358

1811

2264

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

144

192

240

<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:

0.0242

AC:

3678

AN:

152238

Hom.:

Cov.:

AF XY:

0.0252

AC XY:

1879

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.0229

AC:

952

AN:

41540

American (AMR)

AF:

0.0211

AC:

322

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0481

AC:

167

AN:

3470

East Asian (EAS)

AF:

0.0921

AC:

477

AN:

5178

South Asian (SAS)

AF:

0.0554

AC:

267

AN:

4822

European-Finnish (FIN)

AF:

0.0322

AC:

341

AN:

10602

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0153

AC:

1043

AN:

68020

Other (OTH)

AF:

0.0284

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

191

382

572

763

954

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

192

240

<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:

0.0204

Hom.:

Bravo

AF:

0.0229

Asia WGS

AF:

0.0870

AC:

302

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Peroxisome biogenesis disorder 12A (Zellweger) (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

8.5

(source)

DANN

Benign

0.83

PhyloP100

0.066

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over