1-152415009-T-C

Variant names:

• chr1-152415009-T-C
• rs4240877
• ENST00000411804.1:n.95-29835T>C

Variant summary

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

The ENST00000411804.1(CCDST):​n.95-29835T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,146 control chromosomes in the GnomAD database, including 50,373 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 0.81 (50373 hom., cov: 32)
• Consequence: CCDST ENST00000411804.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDST	ENST00000411804.1	n.95-29835T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123299 AN: 152028 Hom.: 50337 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.811 AC: 123391 AN: 152146 Hom.: 50373 Cov.: 32 AF XY: 0.816 AC XY: 60740 AN XY: 74406

African (AFR) AF: 0.728 AC: 30171 AN: 41460

American (AMR) AF: 0.860 AC: 13146 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.848 AC: 2941 AN: 3468

East Asian (EAS) AF: 0.977 AC: 5069 AN: 5188

South Asian (SAS) AF: 0.947 AC: 4574 AN: 4828

European-Finnish (FIN) AF: 0.855 AC: 9061 AN: 10600

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55607 AN: 67996

Other (OTH) AF: 0.825 AC: 1745 AN: 2116

Alfa AF: 0.814 Hom.: 9337

Bravo AF: 0.807

Asia WGS AF: 0.941 AC: 3272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.0
DANN	Benign	0.83
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs4240877; hg19: chr1-152387485;