Variant 11-45909667-T-C 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_004813.4(PEX16):c.*587A>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 0.0678 in 227,992 control chromosomes in the GnomAD database, including 766 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.065 ( 467 hom., cov: 34)

Exomes 𝑓: 0.073 ( 299 hom. )

Consequence

PEX16
NM_004813.4 3_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.124

Variant links:

Genes affected

PEX16 (HGNC:8857): (peroxisomal biogenesis factor 16) The protein encoded by this gene is an integral peroxisomal membrane protein. An inactivating nonsense mutation localized to this gene was observed in a patient with Zellweger syndrome of the complementation group CGD/CG9. Expression of this gene product morphologically and biochemically restores the formation of new peroxisomes, suggesting a role in peroxisome organization and biogenesis. Alternative splicing has been observed for this gene and two variants have been described. [provided by RefSeq, Jul 2008]

PEX16 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=-0.91).

BP6

Variant 11-45909667-T-C is Benign according to our data. Variant chr11-45909667-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 368962.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PEX16	NM_004813.4 linkuse as main transcript	c.*587A>G		3_prime_UTR_variant	11/11	ENST00000378750.10	NP_004804.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PEX16	ENST00000378750.10 linkuse as main transcript	c.*587A>G		3_prime_UTR_variant	11/11	1	NM_004813.4	ENSP00000368024	P1	Q9Y5Y5-1
PEX16	ENST00000241041.7 linkuse as main transcript			downstream_gene_variant		1		ENSP00000241041		Q9Y5Y5-2

Frequencies

GnomAD3 genomes

AF:

0.0653

AC:

9933

AN:

152166

Hom.:

467

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0164

Gnomad AMI

AF:

0.0362

Gnomad AMR

AF:

0.0541

Gnomad ASJ

AF:

0.0291

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0155

Gnomad FIN

AF:

0.144

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0967

Gnomad OTH

AF:

0.0502

GnomAD4 exome

AF:

0.0730

AC:

5527

AN:

75708

Hom.:

299

Cov.:

AF XY:

0.0673

AC XY:

2690

AN XY:

39960

show subpopulations

Gnomad4 AFR exome

AF:

0.0148

Gnomad4 AMR exome

AF:

0.0464

Gnomad4 ASJ exome

AF:

0.0315

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0147

Gnomad4 FIN exome

AF:

0.129

Gnomad4 NFE exome

AF:

0.0974

Gnomad4 OTH exome

AF:

0.0798

GnomAD4 genome

AF:

0.0652

AC:

9930

AN:

152284

Hom.:

467

Cov.:

AF XY:

0.0656

AC XY:

4885

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.0163

Gnomad4 AMR

AF:

0.0541

Gnomad4 ASJ

AF:

0.0291

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0157

Gnomad4 FIN

AF:

0.144

Gnomad4 NFE

AF:

0.0967

Gnomad4 OTH

AF:

0.0497

Alfa

AF:

0.0838

Hom.:

146

Bravo

AF:

0.0559

Asia WGS

AF:

0.00924

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Peroxisome biogenesis disorder 1A (Zellweger)

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

6.4

DANN

Benign

0.39

Splicing

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