17-58244090-GACACACACACACACACACACACACACACAC-GACACACACACACACACACACACACACACACACACACACAC

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_006151.3(LPO):​c.164+42_164+51dupACACACACAC 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 0.00023 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00013 ( 0 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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LPONM_006151.3 linkc.164+42_164+51dupACACACACAC intron_variant Intron 3 of 12 ENST00000262290.9 NP_006142.1 P22079-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LPOENST00000262290.9 linkc.164+42_164+51dupACACACACAC intron_variant Intron 3 of 12 1 NM_006151.3 ENSP00000262290.4 P22079-1

Frequencies

GnomAD3 genomes
AF:
0.000227
AC:
32
AN:
140874
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000377
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000227
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000262
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.000133
AC:
122
AN:
920430
Hom.:
0
Cov.:
0
AF XY:
0.000127
AC XY:
60
AN XY:
473744
show subpopulations
Gnomad4 AFR exome
AF:
0.000329
Gnomad4 AMR exome
AF:
0.000384
Gnomad4 ASJ exome
AF:
0.000227
Gnomad4 EAS exome
AF:
0.000307
Gnomad4 SAS exome
AF:
0.0000554
Gnomad4 FIN exome
AF:
0.0000244
Gnomad4 NFE exome
AF:
0.000103
Gnomad4 OTH exome
AF:
0.000212
GnomAD4 genome
AF:
0.000227
AC:
32
AN:
140974
Hom.:
0
Cov.:
0
AF XY:
0.000279
AC XY:
19
AN XY:
68198
show subpopulations
Gnomad4 AFR
AF:
0.000376
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000227
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000262
Gnomad4 OTH
AF:
0.00

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.

Other links and lift over

dbSNP: rs67390833; hg19: chr17-56321451; API