chr1-150945146-G-GT
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The ENST00000368962.6(SETDB1):c.1179dup(p.Gly394TrpfsTer18) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000577 in 1,612,690 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000058 ( 0 hom. )
Consequence
SETDB1
ENST00000368962.6 frameshift
ENST00000368962.6 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0550
Genes affected
SETDB1 (HGNC:10761): (SET domain bifurcated histone lysine methyltransferase 1) This gene encodes a histone methyltransferase which regulates histone methylation, gene silencing, and transcriptional repression. This gene has been identified as a target for treatment in Huntington Disease, given that gene silencing and transcription dysfunction likely play a role in the disease pathogenesis. Alternatively spliced transcript variants of this gene have been described.[provided by RefSeq, Jun 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant 1-150945146-G-GT is Benign according to our data. Variant chr1-150945146-G-GT is described in ClinVar as [Benign]. Clinvar id is 1292241.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 9 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SETDB1 | NM_001366418.1 | c.1140+39dup | intron_variant | ENST00000692827.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SETDB1 | ENST00000692827.1 | c.1140+39dup | intron_variant | NM_001366418.1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152110Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000443 AC: 11AN: 248268Hom.: 0 AF XY: 0.0000671 AC XY: 9AN XY: 134080
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GnomAD4 exome AF: 0.0000575 AC: 84AN: 1460580Hom.: 0 Cov.: 32 AF XY: 0.0000619 AC XY: 45AN XY: 726452
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GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152110Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74310
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
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Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: -5
Find out detailed SpliceAI scores and Pangolin per-transcript scores at