rs8178407
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006151.3(LPO):c.1694-54A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 1,404,024 control chromosomes in the GnomAD database, including 123,957 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.49 ( 20827 hom., cov: 33)
Exomes 𝑓: 0.40 ( 103130 hom. )
Consequence
LPO
NM_006151.3 intron
NM_006151.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.170
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LPO | NM_006151.3 | c.1694-54A>G | intron_variant | ENST00000262290.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LPO | ENST00000262290.9 | c.1694-54A>G | intron_variant | 1 | NM_006151.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.490 AC: 74522AN: 152022Hom.: 20773 Cov.: 33
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GnomAD4 exome AF: 0.396 AC: 496115AN: 1251884Hom.: 103130 AF XY: 0.397 AC XY: 249942AN XY: 630142
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GnomAD4 genome ? AF: 0.491 AC: 74637AN: 152140Hom.: 20827 Cov.: 33 AF XY: 0.487 AC XY: 36201AN XY: 74360
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at