rs8179078

chr15-89682512-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527

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]

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	#exon/exons	MANE	UniProt
PEX11A	NM_003847.3	c.*865A>G		3_prime_UTR_variant	3/3	ENST00000300056.8
PEX11A	NM_001271572.2	c.*865A>G		3_prime_UTR_variant	3/3
PEX11A	NM_001271573.2	c.*865A>G		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PEX11A	ENST00000300056.8	c.*865A>G		3_prime_UTR_variant	3/3	1	NM_003847.3	P1
PEX11A	ENST00000561224.5	c.173-972A>G		intron_variant		4
PEX11A	ENST00000557982.1	n.207-972A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0748 AC: 11382 AN: 152128 Hom.: 562 Cov.: 32

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: 2 AN: 26 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 2 AN XY: 20

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.111

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0747 AC: 11380 AN: 152246 Hom.: 563 Cov.: 32 AF XY: 0.0749 AC XY: 5575 AN XY: 74430

Gnomad4 AFR AF: 0.0194

Gnomad4 AMR AF: 0.0579

Gnomad4 ASJ AF: 0.0637

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.0657

Gnomad4 FIN AF: 0.0967

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0624

Alfa AF: 0.0927 Hom.: 980

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
Dann	Benign	0.70

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

Other links and lift over

dbSNP: rs8179078; hg19: chr15-90225743;