Genetic Variant LPO:c.164+44_164+51delACACACAC (chr17-58244090-GACACACAC-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 ENST00000262290.9(LPO):c.164+44_164+51delACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00586 in 1,058,936 control chromosomes in the GnomAD database, including 15 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0068 ( 2 hom., cov: 0)

Exomes 𝑓: 0.0057 ( 13 hom. )

Consequence

LPO
ENST00000262290.9 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: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000262290.9. 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+44_164+51delACACACAC	intron	N/A	NP_006142.1
LPO	NM_001160102.2		c.76+1070_76+1077delACACACAC	intron	N/A	NP_001153574.1
LPO	NR_027647.2		n.234+1070_234+1077delACACACAC	intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes

AF:

0.00678

AC:

955

AN:

140878

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00703

Gnomad AMI

AF:

0.00113

Gnomad AMR

AF:

0.00672

Gnomad ASJ

AF:

0.0158

Gnomad EAS

AF:

0.000633

Gnomad SAS

AF:

0.00272

Gnomad FIN

AF:

0.0169

Gnomad MID

AF:

0.0101

Gnomad NFE

AF:

0.00556

Gnomad OTH

AF:

0.00680

GnomAD4 exome

AF:

0.00572

AC:

5253

AN:

917958

Hom.:

AF XY:

0.00577

AC XY:

2727

AN XY:

472410

show subpopulations

African (AFR)

AF:

0.00835

AC:

177

AN:

21208

American (AMR)

AF:

0.00410

AC:

160

AN:

39006

Ashkenazi Jewish (ASJ)

AF:

0.0136

AC:

298

AN:

21980

East Asian (EAS)

AF:

0.00140

AC:

AN:

35838

South Asian (SAS)

AF:

0.00277

AC:

200

AN:

72092

European-Finnish (FIN)

AF:

0.0138

AC:

565

AN:

40846

Middle Eastern (MID)

AF:

0.0124

AC:

AN:

4436

European-Non Finnish (NFE)

AF:

0.00549

AC:

3517

AN:

640162

Other (OTH)

AF:

0.00545

AC:

231

AN:

42390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.424

Heterozygous variant carriers

180

360

541

721

901

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

172

258

344

430

<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:

0.00677

AC:

954

AN:

140978

Hom.:

Cov.:

AF XY:

0.00680

AC XY:

464

AN XY:

68196

show subpopulations

African (AFR)

AF:

0.00701

AC:

261

AN:

37248

American (AMR)

AF:

0.00672

AC:

AN:

14146

Ashkenazi Jewish (ASJ)

AF:

0.0158

AC:

AN:

3362

East Asian (EAS)

AF:

0.000634

AC:

AN:

4732

South Asian (SAS)

AF:

0.00273

AC:

AN:

4398

European-Finnish (FIN)

AF:

0.0169

AC:

153

AN:

9060

Middle Eastern (MID)

AF:

0.0109

AC:

AN:

276

European-Non Finnish (NFE)

AF:

0.00554

AC:

360

AN:

64934

Other (OTH)

AF:

0.00672

AC:

AN:

1934

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

148

197

246

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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

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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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