rs11204949

Variant names:

• chr1-152247321-A-C
• rs11204949
• ENST00000420707.5:n.159-1574A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-152247321-A-C
• chr1-152247321-A-G
• chr1-152247321-A-T

Variant summary

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

The ENST00000420707.5(CCDST):​n.159-1574A>C 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 152,180 control chromosomes in the GnomAD database, including 3,117 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 (3117 hom., cov: 32)
• Consequence: CCDST ENST00000420707.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDST	NR_186761.1	n.354-1574A>C		intron_variant	Intron 1 of 7
CCDST	NR_186762.1	n.179+57840A>C		intron_variant	Intron 1 of 5
CCDST	NR_186763.1	n.206+57813A>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDST	ENST00000420707.5	n.159-1574A>C		intron_variant	Intron 1 of 8	5
CCDST	ENST00000593011.5	n.297-54433A>C		intron_variant	Intron 1 of 3	4
CCDST	ENST00000630125.3	n.179+57840A>C		intron_variant	Intron 1 of 7	5

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23956 AN: 152062 Hom.: 3114 Cov.: 32

Gnomad AFR AF: 0.0385

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.157 AC: 23958 AN: 152180 Hom.: 3117 Cov.: 32 AF XY: 0.169 AC XY: 12558 AN XY: 74390

African (AFR) AF: 0.0385 AC: 1601 AN: 41562

American (AMR) AF: 0.328 AC: 5012 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3468

East Asian (EAS) AF: 0.570 AC: 2949 AN: 5174

South Asian (SAS) AF: 0.369 AC: 1777 AN: 4822

European-Finnish (FIN) AF: 0.174 AC: 1845 AN: 10598

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.134 AC: 9138 AN: 67972

Other (OTH) AF: 0.195 AC: 411 AN: 2112

Alfa AF: 0.138 Hom.: 926

Bravo AF: 0.167

Asia WGS AF: 0.448 AC: 1557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.0
DANN	Benign	0.47
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs11204949; hg19: chr1-152219797;