chr1-152329100-G-A

Variant names:

• chr1-152329100-G-A
• rs1933064
• ENST00000392688.7:n.915-3483G>A

Variant summary

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

The ENST00000392688.7(CCDST):​n.915-3483G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,712 control chromosomes in the GnomAD database, including 27,208 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 0.58 (27208 hom., cov: 32)
• Consequence: CCDST ENST00000392688.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.758
• 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=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDST	NR_103778.1	n.915-3483G>A		intron_variant	Intron 2 of 6
CCDST	NR_186761.1	n.578-3483G>A		intron_variant	Intron 3 of 7
CCDST	NR_186762.1	n.180-3483G>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDST	ENST00000392688.7	n.915-3483G>A		intron_variant	Intron 2 of 6	2
CCDST	ENST00000420707.5	n.515-3483G>A		intron_variant	Intron 5 of 8	5
CCDST	ENST00000593011.5	n.429-3483G>A		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87616 AN: 151594 Hom.: 27159 Cov.: 32

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.578 AC: 87725 AN: 151712 Hom.: 27208 Cov.: 32 AF XY: 0.578 AC XY: 42857 AN XY: 74146

African (AFR) AF: 0.784 AC: 32498 AN: 41444

American (AMR) AF: 0.600 AC: 9136 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1886 AN: 3460

East Asian (EAS) AF: 0.863 AC: 4419 AN: 5118

South Asian (SAS) AF: 0.586 AC: 2818 AN: 4808

European-Finnish (FIN) AF: 0.403 AC: 4257 AN: 10564

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31019 AN: 67786

Other (OTH) AF: 0.564 AC: 1186 AN: 2104

Alfa AF: 0.506 Hom.: 26655

Bravo AF: 0.604

Asia WGS AF: 0.735 AC: 2557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	13
DANN	Benign	0.83
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs1933064; hg19: chr1-152301576;