1-152286602-A-G

Variant names:

• chr1-152286602-A-G
• rs11204971
• ENST00000420707.5:n.383-15152A>G

Variant summary

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

The ENST00000593011.5(CCDST):​n.297-15152A>G variant causes a intron change. The variant allele was found at a frequency of 0.156 in 152,102 control chromosomes in the GnomAD database, including 3,088 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 (3088 hom., cov: 32)
• Consequence: CCDST ENST00000593011.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 9 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000593011.5. 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.577+34844A>G		intron	N/A
	CCDST	NR_186762.1		n.180-45981A>G		intron	N/A
	CCDST	NR_186763.1		n.207-45981A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDST	ENST00000420707.5	TSL:5	n.383-15152A>G		intron	N/A
	CCDST	ENST00000593011.5	TSL:4	n.297-15152A>G		intron	N/A
	CCDST	ENST00000630125.3	TSL:5	n.180-45981A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23726 AN: 151984 Hom.: 3085 Cov.: 32

Gnomad AFR AF: 0.0356

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.174

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: 0.156 AC: 23725 AN: 152102 Hom.: 3088 Cov.: 32 AF XY: 0.168 AC XY: 12457 AN XY: 74366

African (AFR) AF: 0.0356 AC: 1477 AN: 41546

American (AMR) AF: 0.327 AC: 4987 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1002 AN: 3468

East Asian (EAS) AF: 0.571 AC: 2944 AN: 5160

South Asian (SAS) AF: 0.368 AC: 1779 AN: 4832

European-Finnish (FIN) AF: 0.174 AC: 1840 AN: 10576

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

European-Non Finnish (NFE) AF: 0.134 AC: 9087 AN: 67946

Other (OTH) AF: 0.191 AC: 402 AN: 2110

Alfa AF: 0.155 Hom.: 3862

Bravo AF: 0.165

Asia WGS AF: 0.451 AC: 1567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.2
DANN	Benign	0.43

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: rs11204971;

hg19: chr1-152259078;