1-152417976-T-C

Variant names:

• chr1-152417976-T-C
• rs941934
• ENST00000411804.1:n.95-26868T>C

Variant summary

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

The ENST00000411804.1(CCDST):​n.95-26868T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.931 in 152,052 control chromosomes in the GnomAD database, including 65,931 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 0.93 (65931 hom., cov: 29)
• Consequence: CCDST ENST00000411804.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDST	ENST00000411804.1	n.95-26868T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.930 AC: 141367 AN: 151934 Hom.: 65871 Cov.: 29

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.931 AC: 141486 AN: 152052 Hom.: 65931 Cov.: 29 AF XY: 0.933 AC XY: 69325 AN XY: 74300

African (AFR) AF: 0.980 AC: 40658 AN: 41496

American (AMR) AF: 0.956 AC: 14615 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.941 AC: 3265 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5147 AN: 5148

South Asian (SAS) AF: 0.976 AC: 4655 AN: 4768

European-Finnish (FIN) AF: 0.896 AC: 9486 AN: 10586

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.890 AC: 60524 AN: 67982

Other (OTH) AF: 0.938 AC: 1982 AN: 2112

Alfa AF: 0.915 Hom.: 36032

Bravo AF: 0.935

Asia WGS AF: 0.988 AC: 3436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.4
DANN	Benign	0.66
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs941934; hg19: chr1-152390452;