Genetic Variant CCDST:n.151+4475A>G (chr1-152345685-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000445097.2(CCDST):n.151+4475A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,730 control chromosomes in the GnomAD database, including 6,632 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 0.26 ( 6632 hom., cov: 32)

Consequence

CCDST
ENST00000445097.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

Publications

11 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
CCDST	NR_103778.1 link	n.1406+4475A>G	intron_variant	Intron 6 of 6
CCDST	NR_103779.1 link	n.151+4475A>G	intron_variant	Intron 2 of 2
CCDST	NR_186761.1 link	n.1069+4475A>G	intron_variant	Intron 7 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CCDST	ENST00000445097.2 link	n.151+4475A>G	intron_variant	Intron 2 of 2	1
CCDST	ENST00000392688.7 link	n.1406+4475A>G	intron_variant	Intron 6 of 6	2
CCDST	ENST00000629331.1 link	n.61+10246A>G	intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes

AF:

0.264

AC:

39998

AN:

151612

Hom.:

6610

Cov.:

show subpopulations

Gnomad AFR

AF:

0.424

Gnomad AMI

AF:

0.198

Gnomad AMR

AF:

0.335

Gnomad ASJ

AF:

0.300

Gnomad EAS

AF:

0.480

Gnomad SAS

AF:

0.310

Gnomad FIN

AF:

0.141

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.149

Gnomad OTH

AF:

0.266

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

GnomAD4 genome

AF:

0.264

AC:

40053

AN:

151730

Hom.:

6632

Cov.:

AF XY:

0.268

AC XY:

19881

AN XY:

74178

show subpopulations

African (AFR)

AF:

0.425

AC:

17561

AN:

41344

American (AMR)

AF:

0.335

AC:

5101

AN:

15238

Ashkenazi Jewish (ASJ)

AF:

0.300

AC:

1037

AN:

3462

East Asian (EAS)

AF:

0.480

AC:

2468

AN:

5140

South Asian (SAS)

AF:

0.309

AC:

1487

AN:

4818

European-Finnish (FIN)

AF:

0.141

AC:

1484

AN:

10556

Middle Eastern (MID)

AF:

0.276

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.149

AC:

10099

AN:

67856

Other (OTH)

AF:

0.263

AC:

555

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1367

2733

4100

5466

6833

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.263

Hom.:

3986

Bravo

AF:

0.285

Asia WGS

AF:

0.413

AC:

1434

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.26

(source)

DANN

Benign

0.66

PhyloP100

-1.1

Splicing

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

Publications

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1-152345685-A-G

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