rs877776

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000420707.5(CCDST):​n.158+16034C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 151,964 control chromosomes in the GnomAD database, including 39,608 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 0.71 ( 39608 hom., cov: 31)

Consequence

CCDST
ENST00000420707.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.368

Publications

14 publications found
Variant links:
Genes affected
CCDST (HGNC:55988): (cervical cancer associated DHX9 suppressive transcript)

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 (NFE) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCDSTNR_186761.1 linkn.353+15887C>G intron_variant Intron 1 of 7
CCDSTNR_186762.1 linkn.179+16061C>G intron_variant Intron 1 of 5
CCDSTNR_186763.1 linkn.206+16034C>G intron_variant Intron 1 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCDSTENST00000420707.5 linkn.158+16034C>G intron_variant Intron 1 of 8 5
CCDSTENST00000429352.3 linkn.186-318C>G intron_variant Intron 1 of 2 2
CCDSTENST00000593011.5 linkn.296+37122C>G intron_variant Intron 1 of 3 4

Frequencies

GnomAD3 genomes
AF:
0.707
AC:
107373
AN:
151844
Hom.:
39584
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.555
Gnomad AMI
AF:
0.805
Gnomad AMR
AF:
0.607
Gnomad ASJ
AF:
0.682
Gnomad EAS
AF:
0.365
Gnomad SAS
AF:
0.561
Gnomad FIN
AF:
0.817
Gnomad MID
AF:
0.721
Gnomad NFE
AF:
0.841
Gnomad OTH
AF:
0.709
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.707
AC:
107438
AN:
151964
Hom.:
39608
Cov.:
31
AF XY:
0.699
AC XY:
51895
AN XY:
74278
show subpopulations
African (AFR)
AF:
0.555
AC:
22987
AN:
41412
American (AMR)
AF:
0.606
AC:
9250
AN:
15252
Ashkenazi Jewish (ASJ)
AF:
0.682
AC:
2365
AN:
3466
East Asian (EAS)
AF:
0.365
AC:
1890
AN:
5174
South Asian (SAS)
AF:
0.562
AC:
2698
AN:
4798
European-Finnish (FIN)
AF:
0.817
AC:
8632
AN:
10562
Middle Eastern (MID)
AF:
0.712
AC:
208
AN:
292
European-Non Finnish (NFE)
AF:
0.841
AC:
57168
AN:
67986
Other (OTH)
AF:
0.714
AC:
1507
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1420
2841
4261
5682
7102
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
820
1640
2460
3280
4100
<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:
0.778
Hom.:
5549
Bravo
AF:
0.685
Asia WGS
AF:
0.442
AC:
1524
AN:
3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.5
DANN
Benign
0.54
PhyloP100
-0.37

Splicing

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

Publications

Other links and lift over

dbSNP: rs877776; hg19: chr1-152178018; API