rs3120665

Variant names:

• chr1-152344114-A-G
• rs3120665
• ENST00000445097.2:n.151+2904A>G

Variant summary

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

The ENST00000445097.2(CCDST):​n.151+2904A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,922 control chromosomes in the GnomAD database, including 6,640 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 0.26 (6640 hom., cov: 32)
• Consequence: CCDST ENST00000445097.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.892
• Publications: 15 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDST	NR_103778.1	n.1406+2904A>G		intron_variant	Intron 6 of 6
CCDST	NR_103779.1	n.151+2904A>G		intron_variant	Intron 2 of 2
CCDST	NR_186761.1	n.1069+2904A>G		intron_variant	Intron 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDST	ENST00000445097.2	n.151+2904A>G		intron_variant	Intron 2 of 2	1
CCDST	ENST00000392688.7	n.1406+2904A>G		intron_variant	Intron 6 of 6	2
CCDST	ENST00000629331.1	n.61+8675A>G		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40027 AN: 151804 Hom.: 6618 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.264 AC: 40082 AN: 151922 Hom.: 6640 Cov.: 32 AF XY: 0.268 AC XY: 19889 AN XY: 74264

African (AFR) AF: 0.424 AC: 17589 AN: 41452

American (AMR) AF: 0.334 AC: 5097 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1032 AN: 3458

East Asian (EAS) AF: 0.478 AC: 2468 AN: 5158

South Asian (SAS) AF: 0.309 AC: 1487 AN: 4820

European-Finnish (FIN) AF: 0.140 AC: 1481 AN: 10596

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10111 AN: 67878

Other (OTH) AF: 0.264 AC: 557 AN: 2112

Alfa AF: 0.199 Hom.: 11413

Bravo AF: 0.285

Asia WGS AF: 0.413 AC: 1434 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.45
DANN	Benign	0.52
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs3120665; hg19: chr1-152316590;