rs3126091

Variant names:

• chr1-152334862-T-C
• rs3126091
• ENST00000658099.1:n.3387T>C

Variant summary

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

The ENST00000658099.1(CCDST):​n.3387T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 151,684 control chromosomes in the GnomAD database, including 14,474 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 0.37 (14474 hom., cov: 32)
• Consequence: CCDST ENST00000658099.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 7 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDST	NR_103778.1	n.1081-477T>C		intron_variant	Intron 3 of 6
CCDST	NR_186761.1	n.744-477T>C		intron_variant	Intron 4 of 7
CCDST	NR_186762.1	n.346-477T>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDST	ENST00000658099.1	n.3387T>C		non_coding_transcript_exon_variant	Exon 1 of 4
CCDST	ENST00000392688.7	n.1081-477T>C		intron_variant	Intron 3 of 6	2
CCDST	ENST00000420707.5	n.681-477T>C		intron_variant	Intron 6 of 8	5

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55639 AN: 151566 Hom.: 14432 Cov.: 32

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.367 AC: 55729 AN: 151684 Hom.: 14474 Cov.: 32 AF XY: 0.373 AC XY: 27664 AN XY: 74118

African (AFR) AF: 0.699 AC: 28935 AN: 41402

American (AMR) AF: 0.421 AC: 6404 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1121 AN: 3462

East Asian (EAS) AF: 0.627 AC: 3192 AN: 5088

South Asian (SAS) AF: 0.444 AC: 2139 AN: 4822

European-Finnish (FIN) AF: 0.187 AC: 1980 AN: 10566

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 10964 AN: 67826

Other (OTH) AF: 0.344 AC: 723 AN: 2104

Alfa AF: 0.274 Hom.: 1441

Bravo AF: 0.399

Asia WGS AF: 0.575 AC: 1998 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.71
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs3126091; hg19: chr1-152307338;