chr12-69348408-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000239.3(LYZ):c.-1C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0432 in 1,614,034 control chromosomes in the GnomAD database, including 1,989 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.063 ( 454 hom., cov: 32)
Exomes 𝑓: 0.041 ( 1535 hom. )
Consequence
LYZ
NM_000239.3 5_prime_UTR
NM_000239.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.641
Genes affected
LYZ (HGNC:6740): (lysozyme) This gene encodes human lysozyme, whose natural substrate is the bacterial cell wall peptidoglycan (cleaving the beta[1-4]glycosidic linkages between N-acetylmuramic acid and N-acetylglucosamine). Lysozyme is one of the antimicrobial agents found in human milk, and is also present in spleen, lung, kidney, white blood cells, plasma, saliva, and tears. The protein has antibacterial activity against a number of bacterial species. Missense mutations in this gene have been identified in heritable renal amyloidosis. [provided by RefSeq, Oct 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
Variant 12-69348408-C-T is Benign according to our data. Variant chr12-69348408-C-T is described in ClinVar as [Benign]. Clinvar id is 310329.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LYZ | NM_000239.3 | c.-1C>T | 5_prime_UTR_variant | 1/4 | ENST00000261267.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LYZ | ENST00000261267.7 | c.-1C>T | 5_prime_UTR_variant | 1/4 | 1 | NM_000239.3 | P1 | ||
LYZ | ENST00000548839.1 | c.-1C>T | 5_prime_UTR_variant | 1/2 | 2 | ||||
LYZ | ENST00000549690.1 | c.-1C>T | 5_prime_UTR_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0626 AC: 9529AN: 152146Hom.: 452 Cov.: 32
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GnomAD3 exomes AF: 0.0387 AC: 9720AN: 251468Hom.: 325 AF XY: 0.0371 AC XY: 5049AN XY: 135910
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GnomAD4 exome AF: 0.0411 AC: 60119AN: 1461770Hom.: 1535 Cov.: 31 AF XY: 0.0404 AC XY: 29400AN XY: 727180
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GnomAD4 genome ? AF: 0.0626 AC: 9538AN: 152264Hom.: 454 Cov.: 32 AF XY: 0.0605 AC XY: 4503AN XY: 74476
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Familial visceral amyloidosis, Ostertag type Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Dann
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RBP_binding_hub_radar
RBP_regulation_power_radar
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