GeneBe

ENST00000501396.6:n.546+3353A>T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000501396.6(CASC8):​n.546+3353A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

CASC8
ENST00000501396.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0360

Publications

5 publications found
Variant links:
Genes affected
CASC8 (HGNC:45129): (cancer susceptibility 8)
POU5F1B (HGNC:9223): (POU class 5 homeobox 1B) This intronless gene was thought to be a transcribed pseudogene of POU class 5 homeobox 1, however, it has been reported that this gene can encode a functional protein. The encoded protein is nearly the same length as and highly similar to the POU class 5 homeobox 1 transcription factor, has been shown to be a weak transcriptional activator and may play a role in carcinogenesis and eye development. [provided by RefSeq, Apr 2009]
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]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CASC8NR_117100.1 linkn.1176+3353A>T intron_variant Intron 5 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CASC8ENST00000501396.6 linkn.546+3353A>T intron_variant Intron 1 of 2 1
CASC8ENST00000502082.5 linkn.1176+3353A>T intron_variant Intron 5 of 5 1
CASC8ENST00000523825.3 linkn.546+3353A>T intron_variant Intron 1 of 1 1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
3896
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
1794
African (AFR)
AF:
0.00
AC:
0
AN:
106
American (AMR)
AF:
0.00
AC:
0
AN:
88
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
282
East Asian (EAS)
AF:
0.00
AC:
0
AN:
732
South Asian (SAS)
AF:
0.00
AC:
0
AN:
50
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
8
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
22
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
2296
Other (OTH)
AF:
0.00
AC:
0
AN:
312
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
2.3
DANN
Benign
0.74
PhyloP100
0.036

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs6985419; hg19: chr8-128429721; API