17-58244090-GACACACACACACACACACACACAC-GACACACACACAC

Position:

• chr17-58244090-GACACACACACACACACACACACAC-GACACACACACAC

Variant summary

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

The NM_006151.3(LPO):​c.164+40_164+51delACACACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0311 in 1,061,232 control chromosomes in the GnomAD database, including 302 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.027 (71 hom., cov: 0)
  • Exomes 𝑓: 0.032 (231 hom.)
• Consequence: LPO NM_006151.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.713

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]

ENSG00000286788 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPO	NM_006151.3	c.164+40_164+51delACACACACACAC		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+40_164+51delACACACACACAC		intron_variant		1	NM_006151.3	ENSP00000262290.4

Frequencies

GnomAD3 genomes AF: 0.0269 AC: 3793 AN: 140866 Hom.: 72 Cov.: 0

Gnomad AFR AF: 0.00638

Gnomad AMI AF: 0.0113

Gnomad AMR AF: 0.0169

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.0637

Gnomad SAS AF: 0.0911

Gnomad FIN AF: 0.0556

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0302

Gnomad OTH AF: 0.0204

GnomAD3 exomes AF: 0.0447 AC: 6121 AN: 136960 Hom.: 191 AF XY: 0.0486 AC XY: 3578 AN XY: 73692

Gnomad AFR exome AF: 0.00738

Gnomad AMR exome AF: 0.0186

Gnomad ASJ exome AF: 0.0350

Gnomad EAS exome AF: 0.0756

Gnomad SAS exome AF: 0.0942

Gnomad FIN exome AF: 0.0646

Gnomad NFE exome AF: 0.0362

Gnomad OTH exome AF: 0.0411

GnomAD4 exome AF: 0.0317 AC: 29184 AN: 920266 Hom.: 231 AF XY: 0.0336 AC XY: 15937 AN XY: 473642

Gnomad4 AFR exome AF: 0.00447

Gnomad4 AMR exome AF: 0.0147

Gnomad4 ASJ exome AF: 0.0275

Gnomad4 EAS exome AF: 0.0496

Gnomad4 SAS exome AF: 0.0764

Gnomad4 FIN exome AF: 0.0484

Gnomad4 NFE exome AF: 0.0269

Gnomad4 OTH exome AF: 0.0301

GnomAD4 genome AF: 0.0269 AC: 3794 AN: 140966 Hom.: 71 Cov.: 0 AF XY: 0.0296 AC XY: 2017 AN XY: 68186

Gnomad4 AFR AF: 0.00636

Gnomad4 AMR AF: 0.0169

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.0638

Gnomad4 SAS AF: 0.0917

Gnomad4 FIN AF: 0.0556

Gnomad4 NFE AF: 0.0302

Gnomad4 OTH AF: 0.0202

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;