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
NM_006151.3 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.134
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 -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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0263 AC: 3710AN: 140820Hom.: 49 Cov.: 0
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GnomAD3 exomes AF: 0.0435 AC: 5963AN: 136960Hom.: 64 AF XY: 0.0445 AC XY: 3282AN XY: 73692
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GnomAD4 exome AF: 0.0321 AC: 29236AN: 909466Hom.: 127 AF XY: 0.0328 AC XY: 15325AN XY: 467930
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GnomAD4 genome AF: 0.0264 AC: 3716AN: 140920Hom.: 49 Cov.: 0 AF XY: 0.0259 AC XY: 1767AN XY: 68160
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at