17-58244090-GACACACACACACACACACACACACACACAC-GACACACACACACACACACACACACACACACACACACAC

Variant names:

• chr17-58244090-G-GACACACAC
• rs67390833
• NM_006151.3:c.164+44_164+51dupACACACAC

Variant summary

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

The NM_006151.3(LPO):​c.164+44_164+51dupACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0010 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00050 (0 hom.)
  • Failed GnomAD Quality Control
• 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]

ENSG00000286788 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPO	NM_006151.3	c.164+44_164+51dupACACACAC		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+44_164+51dupACACACAC		intron_variant	Intron 3 of 12	1	NM_006151.3	ENSP00000262290.4

Frequencies

GnomAD3 genomes AF: 0.00100 AC: 141 AN: 140878 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00164

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000920

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000211

Gnomad SAS AF: 0.000227

Gnomad FIN AF: 0.000552

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000878

Gnomad OTH AF: 0.00157

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000496 AC: 456 AN: 920264 Hom.: 0 Cov.: 0 AF XY: 0.000473 AC XY: 224 AN XY: 473664

Gnomad4 AFR exome AF: 0.00141

Gnomad4 AMR exome AF: 0.00105

Gnomad4 ASJ exome AF: 0.0000906

Gnomad4 EAS exome AF: 0.000474

Gnomad4 SAS exome AF: 0.000249

Gnomad4 FIN exome AF: 0.000488

Gnomad4 NFE exome AF: 0.000453

Gnomad4 OTH exome AF: 0.000824

GnomAD4 genome AF: 0.00100 AC: 141 AN: 140978 Hom.: 0 Cov.: 0 AF XY: 0.00101 AC XY: 69 AN XY: 68198

Gnomad4 AFR AF: 0.00166

Gnomad4 AMR AF: 0.000848

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000211

Gnomad4 SAS AF: 0.000227

Gnomad4 FIN AF: 0.000552

Gnomad4 NFE AF: 0.000878

Gnomad4 OTH AF: 0.00155

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;