ENST00000420707.5:n.158+3505C>A

Variant names:

• chr1-152193013-C-A
• rs11590365
• ENST00000420707.5:n.158+3505C>A

Variant summary

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

The ENST00000420707.5(CCDST):​n.158+3505C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,064 control chromosomes in the GnomAD database, including 3,124 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 0.16 (3124 hom., cov: 32)
• Consequence: CCDST ENST00000420707.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 2 publications found

Genes affected

CCDST (HGNC:55988): (cervical cancer associated DHX9 suppressive transcript)

ENSG00000293250 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420707.5. 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
	CCDST	NR_186761.1		n.353+3358C>A		intron	N/A
	CCDST	NR_186762.1		n.179+3532C>A		intron	N/A
	CCDST	NR_186763.1		n.206+3505C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDST	ENST00000420707.5	TSL:5	n.158+3505C>A		intron	N/A
	CCDST	ENST00000429352.3	TSL:2	n.185+3532C>A		intron	N/A
	CCDST	ENST00000593011.5	TSL:4	n.296+24593C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23871 AN: 151948 Hom.: 3121 Cov.: 32

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.157 AC: 23870 AN: 152064 Hom.: 3124 Cov.: 32 AF XY: 0.168 AC XY: 12520 AN XY: 74332

African (AFR) AF: 0.0369 AC: 1531 AN: 41482

American (AMR) AF: 0.328 AC: 5008 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1005 AN: 3472

East Asian (EAS) AF: 0.579 AC: 2977 AN: 5146

South Asian (SAS) AF: 0.366 AC: 1765 AN: 4816

European-Finnish (FIN) AF: 0.175 AC: 1853 AN: 10560

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9122 AN: 67998

Other (OTH) AF: 0.190 AC: 402 AN: 2114

Alfa AF: 0.151 Hom.: 1112

Bravo AF: 0.166

Asia WGS AF: 0.445 AC: 1548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.5
DANN	Benign	0.62
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs11590365; hg19: chr1-152165489;