chr12-6971047-A-AG
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP6_Very_Strong
The NM_006331.8(EMG1):c.126dup(p.Leu43AlafsTer20) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Benign (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
EMG1
NM_006331.8 frameshift
NM_006331.8 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.21
Genes affected
EMG1 (HGNC:16912): (EMG1 N1-specific pseudouridine methyltransferase) This gene encodes an essential, conserved eukaryotic protein that methylates pseudouridine in 18S rRNA. The related protein in yeast is a component of the small subunit processome and is essential for biogenesis of the ribosomal 40S subunit. A mutation in this gene has been associated with Bowen-Conradi syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 12-6971047-A-AG is Benign according to our data. Variant chr12-6971047-A-AG is described in ClinVar as [Benign]. Clinvar id is 768510.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-6971047-A-AG is described in Lovd as [Benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EMG1 | NM_006331.8 | c.126dup | p.Leu43AlafsTer20 | frameshift_variant | 1/6 | ENST00000599672.6 | |
EMG1 | NM_001320049.2 | c.126dup | p.Leu43AlafsTer20 | frameshift_variant | 1/5 | ||
EMG1 | NR_135131.2 | n.137dup | non_coding_transcript_exon_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EMG1 | ENST00000599672.6 | c.126dup | p.Leu43AlafsTer20 | frameshift_variant | 1/6 | 1 | NM_006331.8 | P1 | |
EMG1 | ENST00000611981.1 | n.137dup | non_coding_transcript_exon_variant | 1/4 | 2 | ||||
EMG1 | ENST00000620255.1 | n.115dup | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
EMG1 | ENST00000539196.2 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 1.00 AC: 243953AN: 243956Hom.: 121975 AF XY: 1.00 AC XY: 132515AN XY: 132516
GnomAD3 exomes
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GnomAD4 exome Cov.: 32
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32
GnomAD4 genome Cov.: 32
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3478
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Bowen-Conradi syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: -3
Find out detailed SpliceAI scores and Pangolin per-transcript scores at