chr1-152407652-C-T

Variant names:

• chr1-152407652-C-T
• rs1923509
• ENST00000411804.1:n.94+33605C>T

Variant summary

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

The ENST00000411804.1(CCDST):​n.94+33605C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,028 control chromosomes in the GnomAD database, including 2,734 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 0.17 (2734 hom., cov: 32)
  • Exomes 𝑓: 0.063 (0 hom.)
• Consequence: CCDST ENST00000411804.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000411804.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDST	ENST00000411804.1	TSL:3	n.94+33605C>T		intron	N/A
	CCDST	ENST00000628475.2	TSL:5	n.167-102C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26165 AN: 151894 Hom.: 2730 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.192

GnomAD4 exome AF: 0.0625 AC: 1 AN: 16 Hom.: 0 AF XY: 0.0833 AC XY: 1 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0833 AC: 1 AN: 12

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.172 AC: 26177 AN: 152012 Hom.: 2734 Cov.: 32 AF XY: 0.178 AC XY: 13237 AN XY: 74284

African (AFR) AF: 0.130 AC: 5394 AN: 41476

American (AMR) AF: 0.289 AC: 4411 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1022 AN: 3472

East Asian (EAS) AF: 0.416 AC: 2133 AN: 5130

South Asian (SAS) AF: 0.296 AC: 1425 AN: 4812

European-Finnish (FIN) AF: 0.138 AC: 1461 AN: 10560

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9712 AN: 67990

Other (OTH) AF: 0.190 AC: 399 AN: 2102

Alfa AF: 0.140 Hom.: 797

Bravo AF: 0.182

Asia WGS AF: 0.338 AC: 1174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.65
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs1923509; hg19: chr1-152380128;