15-49128693-A-G
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_004236.4(COPS2):c.1187+9T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000492 in 1,423,684 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000049 ( 0 hom. )
Consequence
COPS2
NM_004236.4 intron
NM_004236.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.450
Genes affected
COPS2 (HGNC:30747): (COP9 signalosome subunit 2) Predicted to enable transcription corepressor activity. Involved in protein deneddylation and protein phosphorylation. Located in cytoplasm. Part of 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 -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.29).
BP6
Variant 15-49128693-A-G is Benign according to our data. Variant chr15-49128693-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 756075.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 7 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COPS2 | NM_004236.4 | c.1187+9T>C | intron_variant | ENST00000388901.10 | NP_004227.1 | |||
COPS2 | NM_001143887.2 | c.1208+9T>C | intron_variant | NP_001137359.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COPS2 | ENST00000388901.10 | c.1187+9T>C | intron_variant | 1 | NM_004236.4 | ENSP00000373553.5 | ||||
COPS2 | ENST00000299259.10 | c.1208+9T>C | intron_variant | 1 | ENSP00000299259.6 | |||||
COPS2 | ENST00000542928.5 | c.995+9T>C | intron_variant | 2 | ENSP00000443664.1 | |||||
COPS2 | ENST00000560240.5 | n.138+784T>C | intron_variant | 4 | ENSP00000453546.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00000417 AC: 1AN: 239808Hom.: 0 AF XY: 0.00000771 AC XY: 1AN XY: 129718
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GnomAD4 exome AF: 0.00000492 AC: 7AN: 1423684Hom.: 0 Cov.: 24 AF XY: 0.00000282 AC XY: 2AN XY: 709698
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GnomAD4 genome Cov.: 32
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Jul 03, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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