Genetic Variant LPO:c.164+42_164+51dupACACACACAC (chr17-58244090-G-GACACACACAC) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_006151.3(LPO):c.164+42_164+51dupACACACACAC 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 0.00023 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00013 ( 0 hom. )

Consequence

LPO
NM_006151.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.134

Publications

2 publications found

Variant links:

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]

LPO links:

ENSG00000286788 (HGNC:):

ENSG00000286788 links:

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ACMG classification

Classification was made for transcript

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LPO	NM_006151.3	MANE Select	c.164+42_164+51dupACACACACAC	intron	N/A	NP_006142.1
LPO	NM_001160102.2		c.76+1068_76+1077dupACACACACAC	intron	N/A	NP_001153574.1
LPO	NR_027647.2		n.234+1068_234+1077dupACACACACAC	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LPO	ENST00000262290.9	TSL:1 MANE Select	c.164+42_164+51dupACACACACAC	intron	N/A	ENSP00000262290.4
LPO	ENST00000421678.6	TSL:1	c.76+1068_76+1077dupACACACACAC	intron	N/A	ENSP00000400245.2
LPO	ENST00000578403.5	TSL:1	n.235+42_235+51dupACACACACAC	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.000227

AC:

AN:

140874

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000377

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000227

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000262

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000133

AC:

122

AN:

920430

Hom.:

Cov.:

AF XY:

0.000127

AC XY:

AN XY:

473744

show subpopulations

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

African (AFR)

AF:

0.000329

AC:

AN:

21264

American (AMR)

AF:

0.000384

AC:

AN:

39054

Ashkenazi Jewish (ASJ)

AF:

0.000227

AC:

AN:

22070

East Asian (EAS)

AF:

0.000307

AC:

AN:

35860

South Asian (SAS)

AF:

0.0000554

AC:

AN:

72208

European-Finnish (FIN)

AF:

0.0000244

AC:

AN:

41022

Middle Eastern (MID)

AF:

0.000900

AC:

AN:

4444

European-Non Finnish (NFE)

AF:

0.000103

AC:

AN:

642000

Other (OTH)

AF:

0.000212

AC:

AN:

42508

⚠️ 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.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.362

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000227

AC:

AN:

140974

Hom.:

Cov.:

AF XY:

0.000279

AC XY:

AN XY:

68198

show subpopulations

African (AFR)

AF:

0.000376

AC:

AN:

37246

American (AMR)

AF:

0.00

AC:

AN:

14146

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3362

East Asian (EAS)

AF:

0.00

AC:

AN:

4730

South Asian (SAS)

AF:

0.000227

AC:

AN:

4398

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9060

Middle Eastern (MID)

AF:

0.00

AC:

AN:

276

European-Non Finnish (NFE)

AF:

0.000262

AC:

AN:

64934

Other (OTH)

AF:

0.00

AC:

AN:

1934

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.439

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over