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. The variant received 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
• Publications: 2 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006151.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPO	NM_006151.3	MANE Select	c.164+44_164+51dupACACACAC		intron	N/A	NP_006142.1
	LPO	NM_001160102.2		c.76+1070_76+1077dupACACACAC		intron	N/A	NP_001153574.1
	LPO	NR_027647.2		n.234+1070_234+1077dupACACACAC		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPO	ENST00000262290.9	TSL:1 MANE Select	c.164+44_164+51dupACACACAC		intron	N/A	ENSP00000262290.4
	LPO	ENST00000421678.6	TSL:1	c.76+1070_76+1077dupACACACAC		intron	N/A	ENSP00000400245.2
	LPO	ENST00000578403.5	TSL:1	n.235+44_235+51dupACACACAC		intron	N/A

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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00141 AC: 30 AN: 21256

American (AMR) AF: 0.00105 AC: 41 AN: 39058

Ashkenazi Jewish (ASJ) AF: 0.0000906 AC: 2 AN: 22070

East Asian (EAS) AF: 0.000474 AC: 17 AN: 35846

South Asian (SAS) AF: 0.000249 AC: 18 AN: 72204

European-Finnish (FIN) AF: 0.000488 AC: 20 AN: 41014

Middle Eastern (MID) AF: 0.000450 AC: 2 AN: 4444

European-Non Finnish (NFE) AF: 0.000453 AC: 291 AN: 641880

Other (OTH) AF: 0.000824 AC: 35 AN: 42492

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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

African (AFR) AF: 0.00166 AC: 62 AN: 37246

American (AMR) AF: 0.000848 AC: 12 AN: 14146

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3362

East Asian (EAS) AF: 0.000211 AC: 1 AN: 4732

South Asian (SAS) AF: 0.000227 AC: 1 AN: 4398

European-Finnish (FIN) AF: 0.000552 AC: 5 AN: 9060

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 276

European-Non Finnish (NFE) AF: 0.000878 AC: 57 AN: 64936

Other (OTH) AF: 0.00155 AC: 3 AN: 1934

Alfa AF: 0.00 Hom.: 254

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs67390833; hg19: chr17-56321451;