chr10-100924001-G-GA
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_018121.4(SLF2):c.1006dup(p.Arg336LysfsTer27) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
SLF2
NM_018121.4 frameshift
NM_018121.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.75
Genes affected
SLF2 (HGNC:17814): (SMC5-SMC6 complex localization factor 2) Enables ubiquitin protein ligase binding activity. Involved in several processes, including positive regulation of cellular component organization; positive regulation of double-strand break repair; and protein localization to site of double-strand break. Located in chromatin; nucleoplasm; and site of double-strand break. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 10-100924001-G-GA is Pathogenic according to our data. Variant chr10-100924001-G-GA is described in ClinVar as [Pathogenic]. Clinvar id is 2443709.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLF2 | NM_018121.4 | c.1006dup | p.Arg336LysfsTer27 | frameshift_variant | 5/20 | ENST00000238961.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLF2 | ENST00000238961.9 | c.1006dup | p.Arg336LysfsTer27 | frameshift_variant | 5/20 | 1 | NM_018121.4 | P2 | |
SLF2 | ENST00000370269.3 | c.1006dup | p.Arg336LysfsTer27 | frameshift_variant | 5/19 | 1 | A2 | ||
SLF2 | ENST00000370271.7 | c.1006dup | p.Arg336LysfsTer27 | frameshift_variant | 5/6 | 1 | |||
SLF2 | ENST00000649226.1 | c.1006dup | p.Arg336LysfsTer27 | frameshift_variant, NMD_transcript_variant | 5/21 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 29
GnomAD4 exome
Cov.:
29
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Atelis syndrome 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 09, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.