17-58244090-GACACACACACACACACACACACACACACAC-GACACACACACACACACACAC

Variant names:

• chr17-58244090-GACACACACAC-G
• rs67390833
• NM_006151.3:c.164+42_164+51delACACACACAC

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_006151.3(LPO):​c.164+42_164+51delACACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00145 in 1,061,174 control chromosomes in the GnomAD database, including 4 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0011 (1 hom., cov: 0)
  • Exomes 𝑓: 0.0015 (3 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 Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAdExome4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPO	NM_006151.3	c.164+42_164+51delACACACACAC		intron_variant	Intron 3 of 12	ENST00000262290.9	NP_006142.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPO	ENST00000262290.9	c.164+42_164+51delACACACACAC		intron_variant	Intron 3 of 12	1	NM_006151.3	ENSP00000262290.4

Frequencies

GnomAD3 genomes AF: 0.00114 AC: 160 AN: 140878 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.000942

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000849

Gnomad ASJ AF: 0.00178

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.00113

Gnomad FIN AF: 0.000442

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00132

Gnomad OTH AF: 0.00105

GnomAD4 exome AF: 0.00150 AC: 1377 AN: 920196 Hom.: 3 AF XY: 0.00146 AC XY: 690 AN XY: 473584

Gnomad4 AFR exome AF: 0.000940

Gnomad4 AMR exome AF: 0.00343

Gnomad4 ASJ exome AF: 0.00227

Gnomad4 EAS exome AF: 0.00162

Gnomad4 SAS exome AF: 0.000873

Gnomad4 FIN exome AF: 0.000878

Gnomad4 NFE exome AF: 0.00148

Gnomad4 OTH exome AF: 0.00144

GnomAD4 genome AF: 0.00114 AC: 161 AN: 140978 Hom.: 1 Cov.: 0 AF XY: 0.00113 AC XY: 77 AN XY: 68198

Gnomad4 AFR AF: 0.000940

Gnomad4 AMR AF: 0.000848

Gnomad4 ASJ AF: 0.00178

Gnomad4 EAS AF: 0.00211

Gnomad4 SAS AF: 0.00136

Gnomad4 FIN AF: 0.000442

Gnomad4 NFE AF: 0.00132

Gnomad4 OTH AF: 0.00103

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;