rs750470319
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The NM_031206.7(LAS1L):βc.1791_1793delβ(p.Asp597del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000425 in 1,197,343 control chromosomes in the GnomAD database, including 1 homozygotes. There are 137 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (β β ).
Frequency
Genomes: π 0.0020 ( 0 hom., 55 hem., cov: 24)
Exomes π: 0.00027 ( 1 hom. 82 hem. )
Consequence
LAS1L
NM_031206.7 inframe_deletion
NM_031206.7 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.49
Genes affected
LAS1L (HGNC:25726): (LAS1 like ribosome biogenesis factor) Enables RNA binding activity. Predicted to be involved in maturation of 5.8S rRNA and maturation of LSU-rRNA. Located in membrane. Part of MLL1 complex. Implicated in Wilson-Turner syndrome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP6
?
Variant X-65518120-TTCA-T is Benign according to our data. Variant chrX-65518120-TTCA-T is described in ClinVar as [Benign]. Clinvar id is 533410.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-65518120-TTCA-T is described in Lovd as [Likely_benign].
BS2
?
High Hemizygotes in GnomAd4 at 55 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAS1L | NM_031206.7 | c.1791_1793del | p.Asp597del | inframe_deletion | 12/14 | ENST00000374811.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAS1L | ENST00000374811.8 | c.1791_1793del | p.Asp597del | inframe_deletion | 12/14 | 1 | NM_031206.7 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00196 AC: 219AN: 111975Hom.: 0 Cov.: 24 AF XY: 0.00158 AC XY: 54AN XY: 34159
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GnomAD3 exomes AF: 0.000549 AC: 99AN: 180466Hom.: 1 AF XY: 0.000407 AC XY: 27AN XY: 66394
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GnomAD4 exome AF: 0.000265 AC: 288AN: 1085313Hom.: 1 AF XY: 0.000234 AC XY: 82AN XY: 351151
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GnomAD4 genome ? AF: 0.00197 AC: 221AN: 112030Hom.: 0 Cov.: 24 AF XY: 0.00161 AC XY: 55AN XY: 34224
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Wilson-Turner syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
LAS1L-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 15, 2023 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at