rs761061736
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_031206.7(LAS1L):c.1371C>T(p.Ser457=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000617 in 1,198,493 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 27 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000018 ( 0 hom., 0 hem., cov: 23)
Exomes 𝑓: 0.000066 ( 0 hom. 27 hem. )
Consequence
LAS1L
NM_031206.7 synonymous
NM_031206.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.156
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant X-65523637-G-A is Benign according to our data. Variant chrX-65523637-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 464821.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-65523637-G-A is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=-0.156 with no splicing effect.
BS2
?
High Hemizygotes in GnomAdExome at 5 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAS1L | NM_031206.7 | c.1371C>T | p.Ser457= | synonymous_variant | 11/14 | ENST00000374811.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAS1L | ENST00000374811.8 | c.1371C>T | p.Ser457= | synonymous_variant | 11/14 | 1 | NM_031206.7 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000178 AC: 2AN: 112492Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34640
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GnomAD3 exomes AF: 0.0000572 AC: 9AN: 157265Hom.: 0 AF XY: 0.000104 AC XY: 5AN XY: 48079
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GnomAD4 exome AF: 0.0000663 AC: 72AN: 1086001Hom.: 0 Cov.: 30 AF XY: 0.0000763 AC XY: 27AN XY: 353889
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GnomAD4 genome ? AF: 0.0000178 AC: 2AN: 112492Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34640
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Wilson-Turner syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 30, 2020 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at