chr18-59286982-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000587244.5(CPLX4):c.256-10248G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,090 control chromosomes in the GnomAD database, including 4,764 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.24 ( 4764 hom., cov: 32)
Consequence
CPLX4
ENST00000587244.5 intron
ENST00000587244.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.624
Publications
3 publications found
Genes affected
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|
Ensembl
Frequencies
GnomAD3 genomes AF: 0.243 AC: 36916AN: 151972Hom.: 4765 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
36916
AN:
151972
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.243 AC: 36914AN: 152090Hom.: 4764 Cov.: 32 AF XY: 0.247 AC XY: 18372AN XY: 74312 show subpopulations
GnomAD4 genome
AF:
AC:
36914
AN:
152090
Hom.:
Cov.:
32
AF XY:
AC XY:
18372
AN XY:
74312
show subpopulations
African (AFR)
AF:
AC:
6233
AN:
41526
American (AMR)
AF:
AC:
4399
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
AC:
1042
AN:
3462
East Asian (EAS)
AF:
AC:
1059
AN:
5182
South Asian (SAS)
AF:
AC:
1587
AN:
4816
European-Finnish (FIN)
AF:
AC:
3260
AN:
10530
Middle Eastern (MID)
AF:
AC:
100
AN:
294
European-Non Finnish (NFE)
AF:
AC:
18241
AN:
68004
Other (OTH)
AF:
AC:
563
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1444
2887
4331
5774
7218
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
384
768
1152
1536
1920
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
962
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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