Genetic Variant CCDST:n.383-214G>A (chr1-152301540-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000420707.5(CCDST):n.383-214G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,072 control chromosomes in the GnomAD database, including 3,795 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 0.19 ( 3795 hom., cov: 32)

Consequence

CCDST
ENST00000420707.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0580

Publications

14 publications found

Variant links:

Genes affected

CCDST (HGNC:55988): (cervical cancer associated DHX9 suppressive transcript)

CCDST links:

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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
CCDST	NR_186761.1 link	n.578-31043G>A	intron_variant	Intron 3 of 7
CCDST	NR_186762.1 link	n.180-31043G>A	intron_variant	Intron 1 of 5
CCDST	NR_186763.1 link	n.207-31043G>A	intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CCDST	ENST00000420707.5 link	n.383-214G>A	intron_variant	Intron 3 of 8	5
CCDST	ENST00000593011.5 link	n.297-214G>A	intron_variant	Intron 1 of 3	4
CCDST	ENST00000630125.3 link	n.180-31043G>A	intron_variant	Intron 1 of 7	5

Frequencies

GnomAD3 genomes

AF:

0.187

AC:

28363

AN:

151954

Hom.:

3788

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0816

Gnomad AMI

AF:

0.196

Gnomad AMR

AF:

0.351

Gnomad ASJ

AF:

0.311

Gnomad EAS

AF:

0.596

Gnomad SAS

AF:

0.429

Gnomad FIN

AF:

0.186

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.158

Gnomad OTH

AF:

0.223

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.187

AC:

28376

AN:

152072

Hom.:

3795

Cov.:

AF XY:

0.198

AC XY:

14747

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.0818

AC:

3395

AN:

41494

American (AMR)

AF:

0.351

AC:

5362

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.311

AC:

1080

AN:

3468

East Asian (EAS)

AF:

0.596

AC:

3082

AN:

5172

South Asian (SAS)

AF:

0.428

AC:

2061

AN:

4818

European-Finnish (FIN)

AF:

0.186

AC:

1967

AN:

10564

Middle Eastern (MID)

AF:

0.265

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.158

AC:

10709

AN:

67980

Other (OTH)

AF:

0.219

AC:

463

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1106

2212

3319

4425

5531

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

298

596

894

1192

1490

<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:

0.158

Hom.:

310

Bravo

AF:

0.196

Asia WGS

AF:

0.501

AC:

1738

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

4.1

(source)

DANN

Benign

0.40

PhyloP100

0.058

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over