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

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_006151.3(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
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:

ENSG00000286788 (HGNC:):

ENSG00000286788 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPO	NM_006151.3 link	c.164+44_164+51delACACACAC		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 link	c.164+44_164+51delACACACAC		intron_variant		1	NM_006151.3	ENSP00000262290.4		P22079-1

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

Gnomad4 AFR exome

AF:

0.00835

Gnomad4 AMR exome

AF:

0.00410

Gnomad4 ASJ exome

AF:

0.0136

Gnomad4 EAS exome

AF:

0.00140

Gnomad4 SAS exome

AF:

0.00277

Gnomad4 FIN exome

AF:

0.0138

Gnomad4 NFE exome

AF:

0.00549

Gnomad4 OTH exome

AF:

0.00545

GnomAD4 genome

AF:

0.00677

AC:

954

AN:

140978

Hom.:

Cov.:

AF XY:

0.00680

AC XY:

464

AN XY:

68196

show subpopulations

Gnomad4 AFR

AF:

0.00701

Gnomad4 AMR

AF:

0.00672

Gnomad4 ASJ

AF:

0.0158

Gnomad4 EAS

AF:

0.000634

Gnomad4 SAS

AF:

0.00273

Gnomad4 FIN

AF:

0.0169

Gnomad4 NFE

AF:

0.00554

Gnomad4 OTH

AF:

0.00672

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