rs67390833

chr17-58244090-GACACACACACACACACACACACAC-Gchr17-58244090-GACACACACACACACACACACACAC-GACchr17-58244090-GACACACACACACACACACACACAC-GACACACchr17-58244090-GACACACACACACACACACACACAC-GACACACACchr17-58244090-GACACACACACACACACACACACAC-GACACACACACchr17-58244090-GACACACACACACACACACACACAC-GACACACACACACchr17-58244090-GACACACACACACACACACACACAC-GACACACACACACACchr17-58244090-GACACACACACACACACACACACAC-GACACACACACACACACchr17-58244090-GACACACACACACACACACACACAC-GACACACACACACACACACchr17-58244090-GACACACACACACACACACACACAC-GACACACACACACACACACACchr17-58244090-GACACACACACACACACACACACAC-GACACACACACACACACACACACchr17-58244090-GACACACACACACACACACACACAC-GACACACACACACACACACACACACACchr17-58244090-GACACACACACACACACACACACAC-GACACACACACACACACACACACACACACchr17-58244090-GACACACACACACACACACACACAC-GACACACACACACACACACACACACACACACchr17-58244090-GACACACACACACACACACACACAC-GACACACACACACACACACACACACACACACACchr17-58244090-GACACACACACACACACACACACAC-GACACACACACACACACACACACACACACACACACchr17-58244090-GACACACACACACACACACACACAC-GACACACACACACACACACACACACACACACACACACchr17-58244090-GACACACACACACACACACACACAC-GACACACACACACACACACACACACACACACACACACAC

Variant summary

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

The NM_006151.3(LPO):c.164+28_164+51del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000165 in 1,061,334 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 0.000092 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00018 (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]

(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/exons	MANE	UniProt
LPO	NM_006151.3	c.164+28_164+51del		intron_variant		ENST00000262290.9
LOC124904038	XR_007065862.1	n.669_692del		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPO	ENST00000262290.9	c.164+28_164+51del		intron_variant		1	NM_006151.3	P1
	ENST00000655053.1	n.2619_2642del		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.0000923 AC: 13 AN: 140880 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000221

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000154

Gnomad OTH AF: 0.000523

GnomAD4 exome AF: 0.000176 AC: 162 AN: 920454 Hom.: 0 AF XY: 0.000186 AC XY: 88 AN XY: 473750

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0000453

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000415

Gnomad4 FIN exome AF: 0.000317

Gnomad4 NFE exome AF: 0.000221

Gnomad4 OTH exome AF: 0.0000706

GnomAD4 genome AF: 0.0000923 AC: 13 AN: 140880 Hom.: 0 Cov.: 0 AF XY: 0.000103 AC XY: 7 AN XY: 68088

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000221

Gnomad4 NFE AF: 0.000154

Gnomad4 OTH AF: 0.000523

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;