NM_006151.3:c.164+38_164+51delACACACACACACAC

Variant names:

• chr17-58244090-GACACACACACACAC-G
• rs67390833
• NM_006151.3:c.164+38_164+51delACACACACACACAC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_006151.3(LPO):​c.164+38_164+51delACACACACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00119 in 1,060,920 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00052 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0013 (0 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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPO	NM_006151.3	c.164+38_164+51delACACACACACACAC		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+38_164+51delACACACACACACAC		intron_variant	Intron 3 of 12	1	NM_006151.3	ENSP00000262290.4

Frequencies

GnomAD3 genomes AF: 0.000525 AC: 74 AN: 140876 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000296

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000708

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000211

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00336

Gnomad NFE AF: 0.000908

Gnomad OTH AF: 0.000523

GnomAD4 exome AF: 0.00129 AC: 1186 AN: 919944 Hom.: 0 AF XY: 0.00124 AC XY: 589 AN XY: 473446

Gnomad4 AFR exome AF: 0.000141

Gnomad4 AMR exome AF: 0.000384

Gnomad4 ASJ exome AF: 0.000317

Gnomad4 EAS exome AF: 0.000810

Gnomad4 SAS exome AF: 0.00143

Gnomad4 FIN exome AF: 0.00105

Gnomad4 NFE exome AF: 0.00146

Gnomad4 OTH exome AF: 0.00106

GnomAD4 genome AF: 0.000525 AC: 74 AN: 140976 Hom.: 0 Cov.: 0 AF XY: 0.000513 AC XY: 35 AN XY: 68198

Gnomad4 AFR AF: 0.000295

Gnomad4 AMR AF: 0.0000707

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000211

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000909

Gnomad4 OTH AF: 0.000517

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;