Variant 17-58244090-GACACACACACACACACACACACAC-GACACACACACACACACACACACACACACAC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_006151.3(LPO):c.164+46_164+51dupACACAC 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 0.021 ( 44 hom., cov: 0)

Exomes 𝑓: 0.0095 ( 11 hom. )

Consequence

LPO
NM_006151.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.134

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:

LPO (HGNC:):

LPO links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0211 (2967/140922) while in subpopulation AFR AF= 0.02 (743/37232). AF 95% confidence interval is 0.0188. There are 44 homozygotes in gnomad4. There are 1541 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 44 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPO	NM_006151.3 linkuse as main transcript	c.164+46_164+51dupACACAC		intron_variant		ENST00000262290.9	NP_006142.1	P22079-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPO	ENST00000262290.9 linkuse as main transcript	c.164+46_164+51dupACACAC		intron_variant		1	NM_006151.3	ENSP00000262290.4		P22079-1

Frequencies

GnomAD3 genomes

AF:

0.0210

AC:

2962

AN:

140822

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0200

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0167

Gnomad ASJ

AF:

0.00208

Gnomad EAS

AF:

0.00612

Gnomad SAS

AF:

0.00817

Gnomad FIN

AF:

0.0665

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0197

Gnomad OTH

AF:

0.0162

GnomAD4 exome

AF:

0.00947

AC:

8697

AN:

918194

Hom.:

Cov.:

AF XY:

0.00932

AC XY:

4403

AN XY:

472546

show subpopulations

Gnomad4 AFR exome

AF:

0.0127

Gnomad4 AMR exome

AF:

0.0115

Gnomad4 ASJ exome

AF:

0.00168

Gnomad4 EAS exome

AF:

0.00464

Gnomad4 SAS exome

AF:

0.00462

Gnomad4 FIN exome

AF:

0.0434

Gnomad4 NFE exome

AF:

0.00814

Gnomad4 OTH exome

AF:

0.0108

GnomAD4 genome

AF:

0.0211

AC:

2967

AN:

140922

Hom.:

Cov.:

AF XY:

0.0226

AC XY:

1541

AN XY:

68172

show subpopulations

Gnomad4 AFR

AF:

0.0200

Gnomad4 AMR

AF:

0.0168

Gnomad4 ASJ

AF:

0.00208

Gnomad4 EAS

AF:

0.00655

Gnomad4 SAS

AF:

0.00819

Gnomad4 FIN

AF:

0.0665

Gnomad4 NFE

AF:

0.0197

Gnomad4 OTH

AF:

0.0160

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over