chr3-51420750-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001387579.1(DCAF1):c.2220C>T(p.Ser740Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0049 in 1,614,044 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0045 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0049 ( 32 hom. )
Consequence
DCAF1
NM_001387579.1 synonymous
NM_001387579.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.942
Genes affected
DCAF1 (HGNC:30911): (DDB1 and CUL4 associated factor 1) Enables estrogen receptor binding activity and histone kinase activity (H2A-T120 specific). Involved in cell competition in a multicellular organism; histone H2A-T120 phosphorylation; and negative regulation of transcription by RNA polymerase II. Located in fibrillar center and nucleoplasm. Part of Cul4-RING E3 ubiquitin ligase complex. Colocalizes with COP9 signalosome. [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=-0.8).
BP6
Variant 3-51420750-G-A is Benign according to our data. Variant chr3-51420750-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2653872.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.942 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DCAF1 | NM_001387579.1 | c.2220C>T | p.Ser740Ser | synonymous_variant | 15/25 | ENST00000684031.1 | NP_001374508.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DCAF1 | ENST00000684031.1 | c.2220C>T | p.Ser740Ser | synonymous_variant | 15/25 | NM_001387579.1 | ENSP00000506880.1 | |||
DCAF1 | ENST00000504652.5 | c.2217C>T | p.Ser739Ser | synonymous_variant | 14/25 | 1 | ENSP00000421724.2 | |||
DCAF1 | ENST00000423656.5 | c.2220C>T | p.Ser740Ser | synonymous_variant | 14/25 | 5 | ENSP00000393183.2 |
Frequencies
GnomAD3 genomes AF: 0.00449 AC: 683AN: 152218Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00438 AC: 1092AN: 249270Hom.: 13 AF XY: 0.00449 AC XY: 607AN XY: 135230
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GnomAD4 exome AF: 0.00495 AC: 7231AN: 1461708Hom.: 32 Cov.: 32 AF XY: 0.00491 AC XY: 3570AN XY: 727136
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GnomAD4 genome AF: 0.00448 AC: 682AN: 152336Hom.: 2 Cov.: 32 AF XY: 0.00408 AC XY: 304AN XY: 74504
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | DCAF1: BP4, BP7, BS2 - |
Computational scores
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Benign
CADD
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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