1-152328745-A-G

Variant names:

• chr1-152328745-A-G
• rs1933063
• ENST00000392688.7:n.915-3838A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000392688.7(CCDST):​n.915-3838A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.936 in 151,918 control chromosomes in the GnomAD database, including 66,648 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 0.94 (66648 hom., cov: 31)
• Consequence: CCDST ENST00000392688.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDST	NR_103778.1	n.915-3838A>G		intron_variant	Intron 2 of 6
CCDST	NR_186761.1	n.578-3838A>G		intron_variant	Intron 3 of 7
CCDST	NR_186762.1	n.180-3838A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDST	ENST00000392688.7	n.915-3838A>G		intron_variant	Intron 2 of 6	2
CCDST	ENST00000420707.5	n.515-3838A>G		intron_variant	Intron 5 of 8	5
CCDST	ENST00000593011.5	n.429-3838A>G		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.935 AC: 142001 AN: 151800 Hom.: 66588 Cov.: 31

Gnomad AFR AF: 0.986

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.951

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.978

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.950

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

GnomAD4 genome AF: 0.936 AC: 142120 AN: 151918 Hom.: 66648 Cov.: 31 AF XY: 0.934 AC XY: 69350 AN XY: 74254

African (AFR) AF: 0.986 AC: 40952 AN: 41522

American (AMR) AF: 0.949 AC: 14472 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.951 AC: 3297 AN: 3466

East Asian (EAS) AF: 0.999 AC: 5126 AN: 5130

South Asian (SAS) AF: 0.978 AC: 4718 AN: 4826

European-Finnish (FIN) AF: 0.826 AC: 8753 AN: 10592

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.909 AC: 61663 AN: 67812

Other (OTH) AF: 0.951 AC: 2004 AN: 2108

Alfa AF: 0.949 Hom.: 14548

Bravo AF: 0.948

Asia WGS AF: 0.988 AC: 3437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	10
DANN	Benign	0.84
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1933063; hg19: chr1-152301221;