17-58244090-GACACACACACACACACACACACACACACAC-GACACACACACACACACACACACACACACACACACACAC

Variant summary

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

The NM_006151.3(LPO):​c.164+44_164+51dupACACACAC 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 0.0010 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00050 ( 0 hom. )
Failed GnomAD Quality Control

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+44_164+51dupACACACAC 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+44_164+51dupACACACAC intron_variant Intron 3 of 12 1 NM_006151.3 ENSP00000262290.4 P22079-1

Frequencies

GnomAD3 genomes
AF:
0.00100
AC:
141
AN:
140878
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00164
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000920
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000211
Gnomad SAS
AF:
0.000227
Gnomad FIN
AF:
0.000552
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000878
Gnomad OTH
AF:
0.00157
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000496
AC:
456
AN:
920264
Hom.:
0
Cov.:
0
AF XY:
0.000473
AC XY:
224
AN XY:
473664
show subpopulations
Gnomad4 AFR exome
AF:
0.00141
Gnomad4 AMR exome
AF:
0.00105
Gnomad4 ASJ exome
AF:
0.0000906
Gnomad4 EAS exome
AF:
0.000474
Gnomad4 SAS exome
AF:
0.000249
Gnomad4 FIN exome
AF:
0.000488
Gnomad4 NFE exome
AF:
0.000453
Gnomad4 OTH exome
AF:
0.000824
GnomAD4 genome
AF:
0.00100
AC:
141
AN:
140978
Hom.:
0
Cov.:
0
AF XY:
0.00101
AC XY:
69
AN XY:
68198
show subpopulations
Gnomad4 AFR
AF:
0.00166
Gnomad4 AMR
AF:
0.000848
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000211
Gnomad4 SAS
AF:
0.000227
Gnomad4 FIN
AF:
0.000552
Gnomad4 NFE
AF:
0.000878
Gnomad4 OTH
AF:
0.00155

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