rs72763416
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000081.4(LYST):c.5023+41C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 1,343,810 control chromosomes in the GnomAD database, including 10,497 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.11 ( 969 hom., cov: 32)
Exomes 𝑓: 0.12 ( 9528 hom. )
Consequence
LYST
NM_000081.4 intron
NM_000081.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.954
Genes affected
LYST (HGNC:1968): (lysosomal trafficking regulator) This gene encodes a protein that regulates intracellular protein trafficking in endosomes, and may be involved in pigmentation. Mutations in this gene are associated with Chediak-Higashi syndrome, a lysosomal storage disorder. Alternative splicing results in multiple transcript variants, though the full-length nature of some of these variants has not been determined. [provided by RefSeq, Apr 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 1-235781886-G-A is Benign according to our data. Variant chr1-235781886-G-A is described in ClinVar as [Benign]. Clinvar id is 254924.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LYST | NM_000081.4 | c.5023+41C>T | intron_variant | ENST00000389793.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LYST | ENST00000389793.7 | c.5023+41C>T | intron_variant | 5 | NM_000081.4 | P1 | |||
LYST | ENST00000489585.5 | c.5023+41C>T | intron_variant, NMD_transcript_variant | 1 | |||||
LYST | ENST00000697178.1 | c.*447+41C>T | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.107 AC: 16254AN: 151952Hom.: 971 Cov.: 32
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GnomAD3 exomes AF: 0.104 AC: 25707AN: 246368Hom.: 1481 AF XY: 0.104 AC XY: 13877AN XY: 133434
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GnomAD4 exome AF: 0.122 AC: 145487AN: 1191738Hom.: 9528 Cov.: 17 AF XY: 0.120 AC XY: 72795AN XY: 605286
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GnomAD4 genome ? AF: 0.107 AC: 16250AN: 152072Hom.: 969 Cov.: 32 AF XY: 0.103 AC XY: 7645AN XY: 74352
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 21% of patients studied by a panel of primary immunodeficiencies. Number of patients: 20. Only high quality variants are reported. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 05, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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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