17-58244090-GACACACACACACACACACACACACACACAC-GACACACACACACACACACACACACACAC

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_006151.3(LPO):​c.164+50_164+51delAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.08 in 1,036,622 control chromosomes in the GnomAD database, including 649 homozygotes. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.081 ( 481 hom., cov: 0)
Exomes 𝑓: 0.080 ( 168 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 Benign. Variant got -9 ACMG points.

BP6
Variant 17-58244090-GAC-G is Benign according to our data. Variant chr17-58244090-GAC-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LPONM_006151.3 linkc.164+50_164+51delAC 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+50_164+51delAC intron_variant Intron 3 of 12 1 NM_006151.3 ENSP00000262290.4 P22079-1

Frequencies

GnomAD3 genomes
AF:
0.0812
AC:
11430
AN:
140690
Hom.:
480
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.110
Gnomad AMI
AF:
0.0968
Gnomad AMR
AF:
0.0704
Gnomad ASJ
AF:
0.0983
Gnomad EAS
AF:
0.0720
Gnomad SAS
AF:
0.0842
Gnomad FIN
AF:
0.0451
Gnomad MID
AF:
0.128
Gnomad NFE
AF:
0.0711
Gnomad OTH
AF:
0.0891
GnomAD3 exomes
AF:
0.110
AC:
15071
AN:
136960
Hom.:
32
AF XY:
0.111
AC XY:
8145
AN XY:
73692
show subpopulations
Gnomad AFR exome
AF:
0.104
Gnomad AMR exome
AF:
0.103
Gnomad ASJ exome
AF:
0.119
Gnomad EAS exome
AF:
0.154
Gnomad SAS exome
AF:
0.119
Gnomad FIN exome
AF:
0.0741
Gnomad NFE exome
AF:
0.106
Gnomad OTH exome
AF:
0.115
GnomAD4 exome
AF:
0.0798
AC:
71447
AN:
895836
Hom.:
168
AF XY:
0.0823
AC XY:
37902
AN XY:
460642
show subpopulations
Gnomad4 AFR exome
AF:
0.0887
Gnomad4 AMR exome
AF:
0.0931
Gnomad4 ASJ exome
AF:
0.125
Gnomad4 EAS exome
AF:
0.165
Gnomad4 SAS exome
AF:
0.108
Gnomad4 FIN exome
AF:
0.0783
Gnomad4 NFE exome
AF:
0.0683
Gnomad4 OTH exome
AF:
0.0935
GnomAD4 genome
AF:
0.0813
AC:
11442
AN:
140786
Hom.:
481
Cov.:
0
AF XY:
0.0797
AC XY:
5428
AN XY:
68108
show subpopulations
Gnomad4 AFR
AF:
0.110
Gnomad4 AMR
AF:
0.0703
Gnomad4 ASJ
AF:
0.0983
Gnomad4 EAS
AF:
0.0720
Gnomad4 SAS
AF:
0.0847
Gnomad4 FIN
AF:
0.0451
Gnomad4 NFE
AF:
0.0711
Gnomad4 OTH
AF:
0.0887

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.060
Details are displayed if max score is > 0.2

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