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
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 -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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0812 AC: 11430AN: 140690Hom.: 480 Cov.: 0
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GnomAD3 exomes AF: 0.110 AC: 15071AN: 136960Hom.: 32 AF XY: 0.111 AC XY: 8145AN XY: 73692
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GnomAD4 exome AF: 0.0798 AC: 71447AN: 895836Hom.: 168 AF XY: 0.0823 AC XY: 37902AN XY: 460642
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GnomAD4 genome AF: 0.0813 AC: 11442AN: 140786Hom.: 481 Cov.: 0 AF XY: 0.0797 AC XY: 5428AN XY: 68108
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ClinVar
Not reported inComputational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at