chr1-152301540-G-A

Variant names:

• chr1-152301540-G-A
• rs12730241
• ENST00000420707.5:n.383-214G>A

Variant summary

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

The ENST00000593011.5(CCDST):​n.297-214G>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 ENST00000593011.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 14 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000593011.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDST	NR_186761.1		n.578-31043G>A		intron	N/A
	CCDST	NR_186762.1		n.180-31043G>A		intron	N/A
	CCDST	NR_186763.1		n.207-31043G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDST	ENST00000420707.5	TSL:5	n.383-214G>A		intron	N/A
	CCDST	ENST00000593011.5	TSL:4	n.297-214G>A		intron	N/A
	CCDST	ENST00000630125.3	TSL:5	n.180-31043G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28363 AN: 151954 Hom.: 3788 Cov.: 32

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.: 32 AF XY: 0.198 AC XY: 14747 AN XY: 74338

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: 78 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10709 AN: 67980

Other (OTH) AF: 0.219 AC: 463 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.1
DANN	Benign	0.40
PhyloP100		0.058

Splicing

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

Other links and lift over

dbSNP: rs12730241; hg19: chr1-152274016;