rs7003345

Variant names:

• chr8-127255532-T-A
• rs7003345
• ENST00000644021.1:n.148+10748T>A

Variant summary

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

The NR_117099.1(CASC21):​n.148+10748T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,126 control chromosomes in the GnomAD database, including 9,353 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 0.32 (9353 hom., cov: 32)
• Consequence: CASC21 NR_117099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.487
• Publications: 2 publications found

Genes affected

PCAT1 (HGNC:43022): (prostate cancer associated transcript 1) This gene produces a long non-coding RNA that promotes cell proliferation and is upregulated in prostate, colorectal, and other cancers. This RNA negatively regulates the BRCA2 tumor suppressor protein and positively regulates Myc oncoprotein. It contains binding sites for microRNAs, and may act as a sponge for microRNAs that regulate cell growth pathways. [provided by RefSeq, Dec 2017]

ENSG00000287781 (HGNC:):

CASC21 (HGNC:49836): (cancer susceptibility 21)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_117099.1. 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
	CASC21	NR_117099.1		n.148+10748T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCAT1	ENST00000644021.1		n.148+10748T>A		intron	N/A
	PCAT1	ENST00000645463.1		n.856-37280T>A		intron	N/A
	PCAT1	ENST00000646670.1		n.1065-83749T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48578 AN: 152008 Hom.: 9315 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.320 AC: 48677 AN: 152126 Hom.: 9353 Cov.: 32 AF XY: 0.319 AC XY: 23719 AN XY: 74358

African (AFR) AF: 0.530 AC: 21968 AN: 41472

American (AMR) AF: 0.344 AC: 5260 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 792 AN: 3466

East Asian (EAS) AF: 0.280 AC: 1451 AN: 5174

South Asian (SAS) AF: 0.222 AC: 1070 AN: 4824

European-Finnish (FIN) AF: 0.247 AC: 2620 AN: 10586

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14428 AN: 67992

Other (OTH) AF: 0.311 AC: 656 AN: 2112

Alfa AF: 0.278 Hom.: 886

Bravo AF: 0.344

Asia WGS AF: 0.310 AC: 1079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.3
DANN	Benign	0.53
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs7003345; hg19: chr8-128267777;