Variant 8-127294837-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000501396.5(CASC8):n.687-4777G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 152,106 control chromosomes in the GnomAD database, including 19,348 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 0.49 ( 19348 hom., cov: 32)

Consequence

CASC8
ENST00000501396.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.31

Variant links:

Genes affected

CASC8 (HGNC:45129): (cancer susceptibility 8)

CASC8 links:

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]

PCAT1 links:

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

CASC21 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC21	NR_117099.1 link	n.149-27236C>T		intron_variant
CASC8	NR_117100.1 link	n.1177-4777G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
CASC8	ENST00000501396.5 link	n.687-4777G>A	intron_variant	1
CASC8	ENST00000502082.5 link	n.1177-4777G>A	intron_variant	1
CASC8	ENST00000523825.2 link	n.547-4777G>A	intron_variant	1

Frequencies

GnomAD3 genomes

AF:

0.486

AC:

73872

AN:

151988

Hom.:

19340

Cov.:

show subpopulations

Gnomad AFR

AF:

0.287

Gnomad AMI

AF:

0.431

Gnomad AMR

AF:

0.570

Gnomad ASJ

AF:

0.579

Gnomad EAS

AF:

0.318

Gnomad SAS

AF:

0.459

Gnomad FIN

AF:

0.545

Gnomad MID

AF:

0.563

Gnomad NFE

AF:

0.588

Gnomad OTH

AF:

0.524

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

GnomAD4 genome

AF:

0.486

AC:

73907

AN:

152106

Hom.:

19348

Cov.:

AF XY:

0.482

AC XY:

35824

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.287

Gnomad4 AMR

AF:

0.570

Gnomad4 ASJ

AF:

0.579

Gnomad4 EAS

AF:

0.318

Gnomad4 SAS

AF:

0.461

Gnomad4 FIN

AF:

0.545

Gnomad4 NFE

AF:

0.588

Gnomad4 OTH

AF:

0.520

Alfa

AF:

0.566

Hom.:

34205

Bravo

AF:

0.480

Asia WGS

AF:

0.362

AC:

1260

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Benign

0.58

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over