rs16902056

chr8-127265394-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_117099.1(CASC21):n.148+20610A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.064 in 152,322 control chromosomes in the GnomAD database, including 374 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 0.064 (374 hom., cov: 32)
• Consequence: CASC21 NR_117099.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186

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]

CASC21 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC21	NR_117099.1	n.148+20610A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCAT1	ENST00000645463.1	n.856-27418A>C		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000644021.1	n.148+20610A>C		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000646670.1	n.1065-73887A>C		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000647190.2	n.1192-27418A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0640 AC: 9737 AN: 152204 Hom.: 369 Cov.: 32

Gnomad AFR AF: 0.0495

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0471

Gnomad ASJ AF: 0.0901

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0530

Gnomad FIN AF: 0.0698

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0806

Gnomad OTH AF: 0.0616

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

GnomAD4 genome AF: 0.0640 AC: 9754 AN: 152322 Hom.: 374 Cov.: 32 AF XY: 0.0636 AC XY: 4736 AN XY: 74492

Gnomad4 AFR AF: 0.0496

Gnomad4 AMR AF: 0.0470

Gnomad4 ASJ AF: 0.0901

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0529

Gnomad4 FIN AF: 0.0698

Gnomad4 NFE AF: 0.0806

Gnomad4 OTH AF: 0.0643

Alfa AF: 0.0728 Hom.: 126

Bravo AF: 0.0607

Asia WGS AF: 0.0370 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.0
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16902056; hg19: chr8-128277639;