rs761960683
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_147129.5(ALS2CL):c.2583del(p.Tyr861Ter) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,780 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
ALS2CL
NM_147129.5 frameshift
NM_147129.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.36
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALS2CL | NM_147129.5 | c.2583del | p.Tyr861Ter | frameshift_variant | 24/26 | ENST00000318962.9 | |
ALS2CL | NM_001190707.2 | c.2583del | p.Tyr861Ter | frameshift_variant | 24/26 | ||
ALS2CL | NR_033815.3 | n.2931del | non_coding_transcript_exon_variant | 24/26 | |||
ALS2CL | NR_135622.2 | n.3519del | non_coding_transcript_exon_variant | 23/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALS2CL | ENST00000318962.9 | c.2583del | p.Tyr861Ter | frameshift_variant | 24/26 | 1 | NM_147129.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251258Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135812
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461780Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1AN XY: 727182
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GnomAD4 genome ? Cov.: 32
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: No evidence that LOF in the gene is disease-causing. - |
Computational scores
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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