GeneBe

rs56720201

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_022457.7(COP1):​c.1142-15_1142-8delTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000838 in 1,192,932 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 30)
Exomes 𝑓: 8.4e-7 ( 0 hom. )

Consequence

COP1
NM_022457.7 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.36

Publications

0 publications found
Variant links:
Genes affected
COP1 (HGNC:17440): (COP1 E3 ubiquitin ligase) Enables ubiquitin protein ligase activity. Involved in positive regulation of proteasomal ubiquitin-dependent protein catabolic process; proteasome-mediated ubiquitin-dependent protein catabolic process; and response to ionizing radiation. Part of Cul4A-RING E3 ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022457.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
COP1
NM_022457.7
MANE Select
c.1142-15_1142-8delTTTTTTTT
splice_region intron
N/ANP_071902.2
COP1
NM_001001740.4
c.1070-15_1070-8delTTTTTTTT
splice_region intron
N/ANP_001001740.1Q8NHY2-2
COP1
NM_001286644.2
c.422-15_422-8delTTTTTTTT
splice_region intron
N/ANP_001273573.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
COP1
ENST00000367669.8
TSL:1 MANE Select
c.1142-15_1142-8delTTTTTTTT
splice_region intron
N/AENSP00000356641.3Q8NHY2-1
COP1
ENST00000308769.12
TSL:1
c.1070-15_1070-8delTTTTTTTT
splice_region intron
N/AENSP00000310943.8Q8NHY2-2
COP1
ENST00000367667.5
TSL:1
n.*318-15_*318-8delTTTTTTTT
splice_region intron
N/AENSP00000356639.1H0Y340

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
AF:
8.38e-7
AC:
1
AN:
1192932
Hom.:
0
AF XY:
0.00000169
AC XY:
1
AN XY:
592366
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
26132
American (AMR)
AF:
0.00
AC:
0
AN:
25848
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
19960
East Asian (EAS)
AF:
0.00
AC:
0
AN:
34966
South Asian (SAS)
AF:
0.00
AC:
0
AN:
59702
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
39570
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4754
European-Non Finnish (NFE)
AF:
0.00000107
AC:
1
AN:
932374
Other (OTH)
AF:
0.00
AC:
0
AN:
49626
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs56720201; hg19: chr1-176050430; API