17-58244090-GACACACACACACACACACACACAC-GACACACACACACACACACAC

Position:

• chr17-58244090-GACACACACACACACACACACACAC-GACACACACACACACACACAC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_006151.3(LPO):​c.164+48_164+51delACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 1,049,340 control chromosomes in the GnomAD database, including 5,643 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.22 (3519 hom., cov: 0)
  • Exomes 𝑓: 0.14 (2124 hom.)
• Consequence: LPO NM_006151.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

Genes affected

LPO (HGNC:6678): (lactoperoxidase) This gene encodes a member of the peroxidase family of proteins. The encoded preproprotein is proteolytically processed to generate the mature enzyme. Following its secretion from salivary, mammary, and other mucosal glands, this enzyme catalyzes the generation of the antimicrobial substance hypothiocyanous acid. This gene is present in a gene cluster on chromosome 17. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed. [provided by RefSeq, Jan 2016]

LPO (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPO	NM_006151.3	c.164+48_164+51delACAC		intron_variant		ENST00000262290.9	NP_006142.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPO	ENST00000262290.9	c.164+48_164+51delACAC		intron_variant		1	NM_006151.3	ENSP00000262290.4

Frequencies

GnomAD3 genomes AF: 0.222 AC: 31221 AN: 140668 Hom.: 3519 Cov.: 0

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.0486

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.265

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.233

GnomAD3 exomes AF: 0.168 AC: 23042 AN: 136960 Hom.: 634 AF XY: 0.171 AC XY: 12618 AN XY: 73692

Gnomad AFR exome AF: 0.143

Gnomad AMR exome AF: 0.124

Gnomad ASJ exome AF: 0.188

Gnomad EAS exome AF: 0.0579

Gnomad SAS exome AF: 0.140

Gnomad FIN exome AF: 0.185

Gnomad NFE exome AF: 0.211

Gnomad OTH exome AF: 0.184

GnomAD4 exome AF: 0.140 AC: 127344 AN: 908572 Hom.: 2124 AF XY: 0.144 AC XY: 67207 AN XY: 467390

Gnomad4 AFR exome AF: 0.125

Gnomad4 AMR exome AF: 0.110

Gnomad4 ASJ exome AF: 0.177

Gnomad4 EAS exome AF: 0.0570

Gnomad4 SAS exome AF: 0.128

Gnomad4 FIN exome AF: 0.201

Gnomad4 NFE exome AF: 0.142

Gnomad4 OTH exome AF: 0.160

GnomAD4 genome AF: 0.222 AC: 31238 AN: 140768 Hom.: 3519 Cov.: 0 AF XY: 0.217 AC XY: 14781 AN XY: 68072

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.0487

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.231

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		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: rs67390833; hg19: chr17-56321451;