rs12088737
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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.11039-24C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0157 in 1,613,624 control chromosomes in the GnomAD database, including 3,018 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.079 ( 1539 hom., cov: 31)
Exomes 𝑓: 0.0091 ( 1479 hom. )
Consequence
LYST
NM_000081.4 intron
NM_000081.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.236
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=-0.74).
BP6
?
Variant 1-235664645-G-A is Benign according to our data. Variant chr1-235664645-G-A is described in ClinVar as [Benign]. Clinvar id is 254909.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LYST | NM_000081.4 | c.11039-24C>T | intron_variant | ENST00000389793.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LYST | ENST00000389793.7 | c.11039-24C>T | intron_variant | 5 | NM_000081.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0787 AC: 11963AN: 152014Hom.: 1536 Cov.: 31
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GnomAD3 exomes AF: 0.0227 AC: 5669AN: 249812Hom.: 673 AF XY: 0.0173 AC XY: 2342AN XY: 135242
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GnomAD4 exome AF: 0.00906 AC: 13247AN: 1461492Hom.: 1479 Cov.: 32 AF XY: 0.00831 AC XY: 6041AN XY: 727066
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GnomAD4 genome ? AF: 0.0789 AC: 12008AN: 152132Hom.: 1539 Cov.: 31 AF XY: 0.0761 AC XY: 5661AN XY: 74382
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2018 | - - |
Computational 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