Genetic Variant LPO:c.164+30_164+51delACACACACACACACACACACAC (chr17-58244090-GACACACACACACACACACACAC-G) – 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+30_164+51delACACACACACACACACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000754 in 1,061,344 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000071 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0000076 ( 0 hom. )

Consequence

LPO
NM_006151.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.713

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	UniProt
LPO	NM_006151.3	MANE Select	c.164+30_164+51delACACACACACACACACACACAC	intron	N/A	NP_006142.1	P22079-1
LPO	NM_001160102.2		c.76+1056_76+1077delACACACACACACACACACACAC	intron	N/A	NP_001153574.1	P22079-2
LPO	NR_027647.2		n.234+1056_234+1077delACACACACACACACACACACAC	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LPO	ENST00000262290.9	TSL:1 MANE Select	c.164+30_164+51delACACACACACACACACACACAC	intron	N/A	ENSP00000262290.4	P22079-1
LPO	ENST00000421678.6	TSL:1	c.76+1056_76+1077delACACACACACACACACACACAC	intron	N/A	ENSP00000400245.2	P22079-2
LPO	ENST00000578403.5	TSL:1	n.235+30_235+51delACACACACACACACACACACAC	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00000710

AC:

AN:

140880

Hom.:

Cov.:

show subpopulations

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:

0.000227

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000760

AC:

AN:

920464

Hom.:

AF XY:

0.00000422

AC XY:

AN XY:

473758

show subpopulations

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

African (AFR)

AF:

0.00

AC:

AN:

21272

American (AMR)

AF:

0.00

AC:

AN:

39060

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

22070

East Asian (EAS)

AF:

0.00

AC:

AN:

35860

South Asian (SAS)

AF:

0.00

AC:

AN:

72208

European-Finnish (FIN)

AF:

0.00

AC:

AN:

41020

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4446

European-Non Finnish (NFE)

AF:

0.00000935

AC:

AN:

642020

Other (OTH)

AF:

0.0000235

AC:

AN:

42508

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0169110), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.375

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:

0.00000710

AC:

AN:

140880

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

68088

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

37136

American (AMR)

AF:

0.00

AC:

AN:

14130

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3362

East Asian (EAS)

AF:

0.00

AC:

AN:

4742

South Asian (SAS)

AF:

0.000227

AC:

AN:

4408

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9060

Middle Eastern (MID)

AF:

0.00

AC:

AN:

298

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

64944

Other (OTH)

AF:

0.00

AC:

AN:

1912

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

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

0.71

Splicing

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

Publications

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17-58244090-GACACACACACACACACACACACACACACAC-GACACACAC

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