rs4845766

Variant names:

• chr1-152418806-C-A
• rs4845766
• ENST00000411804.1:n.95-26038C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-152418806-C-A
• chr1-152418806-C-G

Variant summary

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

The ENST00000411804.1(CCDST):​n.95-26038C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 151,952 control chromosomes in the GnomAD database, including 27,424 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 0.59 (27424 hom., cov: 32)
• Consequence: CCDST ENST00000411804.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534
• Publications: 3 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDST	ENST00000411804.1	TSL:3	n.95-26038C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89548 AN: 151834 Hom.: 27404 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.590 AC: 89596 AN: 151952 Hom.: 27424 Cov.: 32 AF XY: 0.591 AC XY: 43870 AN XY: 74266

African (AFR) AF: 0.425 AC: 17598 AN: 41422

American (AMR) AF: 0.552 AC: 8437 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1920 AN: 3470

East Asian (EAS) AF: 0.564 AC: 2909 AN: 5162

South Asian (SAS) AF: 0.651 AC: 3132 AN: 4814

European-Finnish (FIN) AF: 0.717 AC: 7575 AN: 10558

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45872 AN: 67936

Other (OTH) AF: 0.614 AC: 1294 AN: 2108

Alfa AF: 0.636 Hom.: 15078

Bravo AF: 0.567

Asia WGS AF: 0.594 AC: 2067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.2
DANN	Benign	0.80
PhyloP100		-0.53

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4845766;

hg19: chr1-152391282;