rs3126085

Variant names:

• chr1-152328341-G-A
• rs3126085
• ENST00000392688.7:n.915-4242G>A

Variant summary

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

The ENST00000392688.7(CCDST):​n.915-4242G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 151,842 control chromosomes in the GnomAD database, including 8,737 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 0.29 (8737 hom., cov: 32)
• Consequence: CCDST ENST00000392688.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175
• Publications: 47 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000392688.7. 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_103778.1		n.915-4242G>A		intron	N/A
	CCDST	NR_186761.1		n.578-4242G>A		intron	N/A
	CCDST	NR_186762.1		n.180-4242G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDST	ENST00000392688.7	TSL:2	n.915-4242G>A		intron	N/A
	CCDST	ENST00000420707.5	TSL:5	n.515-4242G>A		intron	N/A
	CCDST	ENST00000593011.5	TSL:4	n.429-4242G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44325 AN: 151724 Hom.: 8714 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.292 AC: 44388 AN: 151842 Hom.: 8737 Cov.: 32 AF XY: 0.300 AC XY: 22275 AN XY: 74212

African (AFR) AF: 0.500 AC: 20715 AN: 41434

American (AMR) AF: 0.375 AC: 5711 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1022 AN: 3460

East Asian (EAS) AF: 0.600 AC: 3076 AN: 5128

South Asian (SAS) AF: 0.384 AC: 1850 AN: 4816

European-Finnish (FIN) AF: 0.180 AC: 1908 AN: 10594

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.137 AC: 9296 AN: 67856

Other (OTH) AF: 0.283 AC: 595 AN: 2102

Alfa AF: 0.201 Hom.: 6248

Bravo AF: 0.316

Asia WGS AF: 0.516 AC: 1796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.33
PhyloP100		0.17

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: rs3126085;

hg19: chr1-152300817;