Genetic Variant LPO:c.164+38_164+51delACACACACACACAC (chr17-58244090-GACACACACACACAC-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+38_164+51delACACACACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00119 in 1,060,920 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 0.00052 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0013 ( 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+38_164+51delACACACACACACAC	intron	N/A	NP_006142.1	P22079-1
LPO	NM_001160102.2		c.76+1064_76+1077delACACACACACACAC	intron	N/A	NP_001153574.1	P22079-2
LPO	NR_027647.2		n.234+1064_234+1077delACACACACACACAC	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LPO	ENST00000262290.9	TSL:1 MANE Select	c.164+38_164+51delACACACACACACAC	intron	N/A	ENSP00000262290.4	P22079-1
LPO	ENST00000421678.6	TSL:1	c.76+1064_76+1077delACACACACACACAC	intron	N/A	ENSP00000400245.2	P22079-2
LPO	ENST00000578403.5	TSL:1	n.235+38_235+51delACACACACACACAC	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.000525

AC:

AN:

140876

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000296

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000708

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000211

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00336

Gnomad NFE

AF:

0.000908

Gnomad OTH

AF:

0.000523

GnomAD4 exome

AF:

0.00129

AC:

1186

AN:

919944

Hom.:

AF XY:

0.00124

AC XY:

589

AN XY:

473446

show subpopulations

African (AFR)

AF:

0.000141

AC:

AN:

21272

American (AMR)

AF:

0.000384

AC:

AN:

39054

Ashkenazi Jewish (ASJ)

AF:

0.000317

AC:

AN:

22064

East Asian (EAS)

AF:

0.000810

AC:

AN:

35814

South Asian (SAS)

AF:

0.00143

AC:

103

AN:

72006

European-Finnish (FIN)

AF:

0.00105

AC:

AN:

40980

Middle Eastern (MID)

AF:

0.00113

AC:

AN:

4444

European-Non Finnish (NFE)

AF:

0.00146

AC:

936

AN:

641828

Other (OTH)

AF:

0.00106

AC:

AN:

42482

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

124

165

206

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

114

152

190

<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:

0.000525

AC:

AN:

140976

Hom.:

Cov.:

AF XY:

0.000513

AC XY:

AN XY:

68198

show subpopulations

African (AFR)

AF:

0.000295

AC:

AN:

37246

American (AMR)

AF:

0.0000707

AC:

AN:

14146

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3362

East Asian (EAS)

AF:

0.000211

AC:

AN:

4732

South Asian (SAS)

AF:

0.00

AC:

AN:

4398

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9058

Middle Eastern (MID)

AF:

0.00362

AC:

AN:

276

European-Non Finnish (NFE)

AF:

0.000909

AC:

AN:

64936

Other (OTH)

AF:

0.000517

AC:

AN:

1934

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

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

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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17-58244090-GACACACACACACACACACACACACACACAC-GACACACACACACACAC

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