rs10489884

Variant names:

• chr1-152345145-G-A
• rs10489884
• ENST00000445097.2:n.151+3935G>A

Variant summary

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

The ENST00000759275.1(CCDST):​n.265G>A 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 0.0961 in 151,966 control chromosomes in the GnomAD database, including 1,754 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 0.096 (1754 hom., cov: 32)
• Consequence: CCDST ENST00000759275.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 0 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000759275.1. 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
	CCDST	NR_103778.1		n.1406+3935G>A		intron	N/A
	CCDST	NR_103779.1		n.151+3935G>A		intron	N/A
	CCDST	NR_186761.1		n.1069+3935G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDST	ENST00000445097.2	TSL:1	n.151+3935G>A		intron	N/A
	CCDST	ENST00000759275.1		n.265G>A		non_coding_transcript_exon	Exon 1 of 2
	CCDST	ENST00000392688.7	TSL:2	n.1406+3935G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0960 AC: 14581 AN: 151848 Hom.: 1750 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0467

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.00868

Gnomad SAS AF: 0.0500

Gnomad FIN AF: 0.00783

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0213

Gnomad OTH AF: 0.0657

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

GnomAD4 genome AF: 0.0961 AC: 14606 AN: 151966 Hom.: 1754 Cov.: 32 AF XY: 0.0934 AC XY: 6936 AN XY: 74280

African (AFR) AF: 0.286 AC: 11847 AN: 41434

American (AMR) AF: 0.0466 AC: 711 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3464

East Asian (EAS) AF: 0.00870 AC: 45 AN: 5170

South Asian (SAS) AF: 0.0501 AC: 241 AN: 4812

European-Finnish (FIN) AF: 0.00783 AC: 83 AN: 10604

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0212 AC: 1442 AN: 67902

Other (OTH) AF: 0.0646 AC: 136 AN: 2106

Alfa AF: 0.0574 Hom.: 311

Bravo AF: 0.107

Asia WGS AF: 0.0440 AC: 153 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	11
DANN	Benign	0.63
PhyloP100		-0.057
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10489884;

hg19: chr1-152317621;