rs877776

Variant names:

• chr1-152205542-C-G
• rs877776
• ENST00000420707.5:n.158+16034C>G

Your query was ambiguous. Multiple possible variants found:

• chr1-152205542-C-G
• chr1-152205542-C-T

Variant summary

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

The ENST00000420707.5(CCDST):​n.158+16034C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 151,964 control chromosomes in the GnomAD database, including 39,608 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 0.71 (39608 hom., cov: 31)
• Consequence: CCDST ENST00000420707.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDST	NR_186761.1	n.353+15887C>G		intron_variant	Intron 1 of 7
CCDST	NR_186762.1	n.179+16061C>G		intron_variant	Intron 1 of 5
CCDST	NR_186763.1	n.206+16034C>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDST	ENST00000420707.5	n.158+16034C>G		intron_variant	Intron 1 of 8	5
CCDST	ENST00000429352.3	n.186-318C>G		intron_variant	Intron 1 of 2	2
CCDST	ENST00000593011.5	n.296+37122C>G		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107373 AN: 151844 Hom.: 39584 Cov.: 31

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.721

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.707 AC: 107438 AN: 151964 Hom.: 39608 Cov.: 31 AF XY: 0.699 AC XY: 51895 AN XY: 74278

African (AFR) AF: 0.555 AC: 22987 AN: 41412

American (AMR) AF: 0.606 AC: 9250 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2365 AN: 3466

East Asian (EAS) AF: 0.365 AC: 1890 AN: 5174

South Asian (SAS) AF: 0.562 AC: 2698 AN: 4798

European-Finnish (FIN) AF: 0.817 AC: 8632 AN: 10562

Middle Eastern (MID) AF: 0.712 AC: 208 AN: 292

European-Non Finnish (NFE) AF: 0.841 AC: 57168 AN: 67986

Other (OTH) AF: 0.714 AC: 1507 AN: 2112

Alfa AF: 0.778 Hom.: 5549

Bravo AF: 0.685

Asia WGS AF: 0.442 AC: 1524 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.54
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs877776; hg19: chr1-152178018;