rs2820421

Positions:

• chr1-160286214-C-A

Variant summary

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

The ENST00000533699.5(PEX19):​n.64+71G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,110 control chromosomes in the GnomAD database, including 32,968 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 0.64 (32962 hom., cov: 32)
  • Exomes 𝑓: 0.59 (6 hom.)
• Consequence: PEX19 ENST00000533699.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

Genes affected

PEX19 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985219	XR_001738265.2	n.492-103C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PEX19	ENST00000533699.5	n.64+71G>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97668 AN: 151958 Hom.: 32913 Cov.: 32

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.637

GnomAD4 exome AF: 0.588 AC: 20 AN: 34 Hom.: 6 AF XY: 0.550 AC XY: 11 AN XY: 20

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.615

GnomAD4 genome AF: 0.643 AC: 97776 AN: 152076 Hom.: 32962 Cov.: 32 AF XY: 0.640 AC XY: 47557 AN XY: 74336

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.639

Alfa AF: 0.582 Hom.: 13998

Bravo AF: 0.654

Asia WGS AF: 0.630 AC: 2193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.81

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2820421; hg19: chr1-160256004;