GeneBe

chr13-46107375-TC-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000415033.4(CPB2-AS1):​n.686-5808delC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.34 ( 8818 hom., cov: 0)

Consequence

CPB2-AS1
ENST00000415033.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.468

Publications

5 publications found
Variant links:
Genes affected
CPB2-AS1 (HGNC:39898): (CPB2 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CPB2-AS1ENST00000415033.4 linkn.686-5808delC intron_variant Intron 3 of 3 3
CPB2-AS1ENST00000624622.2 linkn.980-5808delC intron_variant Intron 4 of 5 6
CPB2-AS1ENST00000653655.1 linkn.310-5808delC intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.338
AC:
51417
AN:
151906
Hom.:
8808
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.346
Gnomad AMI
AF:
0.298
Gnomad AMR
AF:
0.321
Gnomad ASJ
AF:
0.403
Gnomad EAS
AF:
0.182
Gnomad SAS
AF:
0.221
Gnomad FIN
AF:
0.404
Gnomad MID
AF:
0.377
Gnomad NFE
AF:
0.345
Gnomad OTH
AF:
0.341
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.338
AC:
51459
AN:
152024
Hom.:
8818
Cov.:
0
AF XY:
0.338
AC XY:
25127
AN XY:
74318
show subpopulations
African (AFR)
AF:
0.345
AC:
14322
AN:
41462
American (AMR)
AF:
0.321
AC:
4903
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
0.403
AC:
1400
AN:
3472
East Asian (EAS)
AF:
0.182
AC:
944
AN:
5174
South Asian (SAS)
AF:
0.223
AC:
1076
AN:
4822
European-Finnish (FIN)
AF:
0.404
AC:
4272
AN:
10576
Middle Eastern (MID)
AF:
0.371
AC:
109
AN:
294
European-Non Finnish (NFE)
AF:
0.345
AC:
23446
AN:
67936
Other (OTH)
AF:
0.339
AC:
716
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1745
3490
5236
6981
8726
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
498
996
1494
1992
2490
<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:
0.347
Hom.:
1105
Bravo
AF:
0.329
Asia WGS
AF:
0.242
AC:
843
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-0.47

Splicing

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

Publications

Other links and lift over

dbSNP: rs35814191; hg19: chr13-46681510; API