rs201404906
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_000081.4(LYST):c.6122-13del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00416 in 1,609,582 control chromosomes in the GnomAD database, including 229 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.022 ( 122 hom., cov: 32)
Exomes 𝑓: 0.0023 ( 107 hom. )
Consequence
LYST
NM_000081.4 splice_polypyrimidine_tract, intron
NM_000081.4 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.482
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 -16 ACMG points.
BP6
?
Variant 1-235762863-AT-A is Benign according to our data. Variant chr1-235762863-AT-A is described in ClinVar as [Likely_benign]. Clinvar id is 235635.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0734 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LYST | NM_000081.4 | c.6122-13del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000389793.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LYST | ENST00000389793.7 | c.6122-13del | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_000081.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0219 AC: 3320AN: 151924Hom.: 122 Cov.: 32
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GnomAD3 exomes AF: 0.00608 AC: 1503AN: 247242Hom.: 56 AF XY: 0.00448 AC XY: 599AN XY: 133648
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GnomAD4 exome AF: 0.00232 AC: 3376AN: 1457540Hom.: 107 Cov.: 30 AF XY: 0.00203 AC XY: 1473AN XY: 725222
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GnomAD4 genome ? AF: 0.0219 AC: 3324AN: 152042Hom.: 122 Cov.: 32 AF XY: 0.0206 AC XY: 1529AN XY: 74318
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Chédiak-Higashi syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Aug 24, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 14, 2019 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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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