Genetic Variant LPO:c.164+42_164+51delACACACACAC (chr17-58244090-GACACACACAC-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_006151.3(LPO):c.164+42_164+51delACACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00145 in 1,061,174 control chromosomes in the GnomAD database, including 4 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0011 ( 1 hom., cov: 0)

Exomes 𝑓: 0.0015 ( 3 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAdExome4 at 3 AR gene

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+42_164+51delACACACACAC	intron	N/A	NP_006142.1	P22079-1
LPO	NM_001160102.2		c.76+1068_76+1077delACACACACAC	intron	N/A	NP_001153574.1	P22079-2
LPO	NR_027647.2		n.234+1068_234+1077delACACACACAC	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LPO	ENST00000262290.9	TSL:1 MANE Select	c.164+42_164+51delACACACACAC	intron	N/A	ENSP00000262290.4	P22079-1
LPO	ENST00000421678.6	TSL:1	c.76+1068_76+1077delACACACACAC	intron	N/A	ENSP00000400245.2	P22079-2
LPO	ENST00000578403.5	TSL:1	n.235+42_235+51delACACACACAC	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00114

AC:

160

AN:

140878

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000942

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000849

Gnomad ASJ

AF:

0.00178

Gnomad EAS

AF:

0.00211

Gnomad SAS

AF:

0.00113

Gnomad FIN

AF:

0.000442

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00132

Gnomad OTH

AF:

0.00105

GnomAD4 exome

AF:

0.00150

AC:

1377

AN:

920196

Hom.:

AF XY:

0.00146

AC XY:

690

AN XY:

473584

show subpopulations

African (AFR)

AF:

0.000940

AC:

AN:

21266

American (AMR)

AF:

0.00343

AC:

134

AN:

39060

Ashkenazi Jewish (ASJ)

AF:

0.00227

AC:

AN:

22058

East Asian (EAS)

AF:

0.00162

AC:

AN:

35848

South Asian (SAS)

AF:

0.000873

AC:

AN:

72164

European-Finnish (FIN)

AF:

0.000878

AC:

AN:

41006

Middle Eastern (MID)

AF:

0.00113

AC:

AN:

4444

European-Non Finnish (NFE)

AF:

0.00148

AC:

950

AN:

641860

Other (OTH)

AF:

0.00144

AC:

AN:

42490

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.456

Heterozygous variant carriers

148

198

247

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

150

<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:

0.00114

AC:

161

AN:

140978

Hom.:

Cov.:

AF XY:

0.00113

AC XY:

AN XY:

68198

show subpopulations

African (AFR)

AF:

0.000940

AC:

AN:

37248

American (AMR)

AF:

0.000848

AC:

AN:

14146

Ashkenazi Jewish (ASJ)

AF:

0.00178

AC:

AN:

3362

East Asian (EAS)

AF:

0.00211

AC:

AN:

4732

South Asian (SAS)

AF:

0.00136

AC:

AN:

4398

European-Finnish (FIN)

AF:

0.000442

AC:

AN:

9058

Middle Eastern (MID)

AF:

0.00

AC:

AN:

276

European-Non Finnish (NFE)

AF:

0.00132

AC:

AN:

64936

Other (OTH)

AF:

0.00103

AC:

AN:

1934

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.526

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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