1-152415662-C-T

Variant names:

• chr1-152415662-C-T
• rs4845763
• ENST00000411804.1:n.95-29182C>T

Variant summary

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

The ENST00000411804.1(CCDST):​n.95-29182C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 152,190 control chromosomes in the GnomAD database, including 57,735 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 0.87 (57735 hom., cov: 31)
• Consequence: CCDST ENST00000411804.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.609
• Publications: 7 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 = 0.955 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000411804.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDST	ENST00000411804.1	TSL:3	n.95-29182C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.870 AC: 132240 AN: 152072 Hom.: 57678 Cov.: 31

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.870 AC: 132356 AN: 152190 Hom.: 57735 Cov.: 31 AF XY: 0.874 AC XY: 64990 AN XY: 74400

African (AFR) AF: 0.929 AC: 38595 AN: 41528

American (AMR) AF: 0.882 AC: 13497 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2960 AN: 3472

East Asian (EAS) AF: 0.977 AC: 5048 AN: 5166

South Asian (SAS) AF: 0.948 AC: 4572 AN: 4824

European-Finnish (FIN) AF: 0.855 AC: 9052 AN: 10590

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55701 AN: 67994

Other (OTH) AF: 0.875 AC: 1849 AN: 2112

Alfa AF: 0.840 Hom.: 42196

Bravo AF: 0.872

Asia WGS AF: 0.955 AC: 3323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.19
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs4845763; hg19: chr1-152388138;