17-58244090-GACACACACACACACACACACACAC-GACACACACACACACACAC

Variant summary

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

The NM_006151.3(LPO):​c.164+46_164+51delACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0314 in 1,050,386 control chromosomes in the GnomAD database, including 176 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.026 ( 49 hom., cov: 0)
Exomes 𝑓: 0.032 ( 127 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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0264 (3716/140920) while in subpopulation NFE AF= 0.0307 (1991/64910). AF 95% confidence interval is 0.0296. There are 49 homozygotes in gnomad4. There are 1767 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 49 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LPONM_006151.3 linkc.164+46_164+51delACACAC intron_variant ENST00000262290.9 NP_006142.1 P22079-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LPOENST00000262290.9 linkc.164+46_164+51delACACAC intron_variant 1 NM_006151.3 ENSP00000262290.4 P22079-1

Frequencies

GnomAD3 genomes
AF:
0.0263
AC:
3710
AN:
140820
Hom.:
49
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0243
Gnomad AMI
AF:
0.0158
Gnomad AMR
AF:
0.0222
Gnomad ASJ
AF:
0.0226
Gnomad EAS
AF:
0.00443
Gnomad SAS
AF:
0.0127
Gnomad FIN
AF:
0.0315
Gnomad MID
AF:
0.0134
Gnomad NFE
AF:
0.0307
Gnomad OTH
AF:
0.0246
GnomAD3 exomes
AF:
0.0435
AC:
5963
AN:
136960
Hom.:
64
AF XY:
0.0445
AC XY:
3282
AN XY:
73692
show subpopulations
Gnomad AFR exome
AF:
0.0388
Gnomad AMR exome
AF:
0.0191
Gnomad ASJ exome
AF:
0.0447
Gnomad EAS exome
AF:
0.00838
Gnomad SAS exome
AF:
0.0236
Gnomad FIN exome
AF:
0.0609
Gnomad NFE exome
AF:
0.0632
Gnomad OTH exome
AF:
0.0459
GnomAD4 exome
AF:
0.0321
AC:
29236
AN:
909466
Hom.:
127
AF XY:
0.0328
AC XY:
15325
AN XY:
467930
show subpopulations
Gnomad4 AFR exome
AF:
0.0301
Gnomad4 AMR exome
AF:
0.0169
Gnomad4 ASJ exome
AF:
0.0332
Gnomad4 EAS exome
AF:
0.00518
Gnomad4 SAS exome
AF:
0.0192
Gnomad4 FIN exome
AF:
0.0467
Gnomad4 NFE exome
AF:
0.0350
Gnomad4 OTH exome
AF:
0.0358
GnomAD4 genome
AF:
0.0264
AC:
3716
AN:
140920
Hom.:
49
Cov.:
0
AF XY:
0.0259
AC XY:
1767
AN XY:
68160
show subpopulations
Gnomad4 AFR
AF:
0.0245
Gnomad4 AMR
AF:
0.0221
Gnomad4 ASJ
AF:
0.0226
Gnomad4 EAS
AF:
0.00444
Gnomad4 SAS
AF:
0.0125
Gnomad4 FIN
AF:
0.0315
Gnomad4 NFE
AF:
0.0307
Gnomad4 OTH
AF:
0.0238

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