chr10-35049745-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_003591.4(CUL2):c.444G>A(p.Arg148=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00598 in 1,612,868 control chromosomes in the GnomAD database, including 445 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.030 ( 223 hom., cov: 32)
Exomes 𝑓: 0.0035 ( 222 hom. )
Consequence
CUL2
NM_003591.4 synonymous
NM_003591.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.09
Genes affected
CUL2 (HGNC:2552): (cullin 2) Enables ubiquitin protein ligase binding activity. Predicted to be involved in SCF-dependent proteasomal ubiquitin-dependent protein catabolic process and protein ubiquitination. Predicted to act upstream of or within protein catabolic process. Located in nucleoplasm. Part of Cul2-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BP6
?
Variant 10-35049745-C-T is Benign according to our data. Variant chr10-35049745-C-T is described in ClinVar as [Benign]. Clinvar id is 776506.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.09 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CUL2 | NM_003591.4 | c.444G>A | p.Arg148= | synonymous_variant | 6/21 | ENST00000374749.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CUL2 | ENST00000374749.8 | c.444G>A | p.Arg148= | synonymous_variant | 6/21 | 1 | NM_003591.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0296 AC: 4504AN: 152118Hom.: 223 Cov.: 32
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GnomAD3 exomes AF: 0.00757 AC: 1888AN: 249544Hom.: 86 AF XY: 0.00533 AC XY: 719AN XY: 134798
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GnomAD4 exome AF: 0.00351 AC: 5124AN: 1460632Hom.: 222 Cov.: 30 AF XY: 0.00304 AC XY: 2211AN XY: 726526
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GnomAD4 genome ? AF: 0.0297 AC: 4514AN: 152236Hom.: 223 Cov.: 32 AF XY: 0.0289 AC XY: 2152AN XY: 74462
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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 | Invitae | May 08, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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