rs779407196
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_031206.7(LAS1L):āc.99G>Cā(p.Ser33=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000244 in 1,198,809 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 71 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.000072 ( 0 hom., 2 hem., cov: 23)
Exomes š: 0.00026 ( 0 hom. 69 hem. )
Consequence
LAS1L
NM_031206.7 synonymous
NM_031206.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0650
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=-0.69).
BP6
?
Variant X-65534617-C-G is Benign according to our data. Variant chrX-65534617-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 464826.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.065 with no splicing effect.
BS2
?
High Hemizygotes in GnomAd4 at 2 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAS1L | NM_031206.7 | c.99G>C | p.Ser33= | synonymous_variant | 1/14 | ENST00000374811.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAS1L | ENST00000374811.8 | c.99G>C | p.Ser33= | synonymous_variant | 1/14 | 1 | NM_031206.7 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000718 AC: 8AN: 111402Hom.: 0 Cov.: 23 AF XY: 0.0000596 AC XY: 2AN XY: 33574
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GnomAD3 exomes AF: 0.000106 AC: 17AN: 159793Hom.: 0 AF XY: 0.0000200 AC XY: 1AN XY: 50051
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GnomAD4 exome AF: 0.000261 AC: 284AN: 1087407Hom.: 0 Cov.: 31 AF XY: 0.000194 AC XY: 69AN XY: 355035
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GnomAD4 genome ? AF: 0.0000718 AC: 8AN: 111402Hom.: 0 Cov.: 23 AF XY: 0.0000596 AC XY: 2AN XY: 33574
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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 | Aug 19, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at