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GeneBe

rs16901979

Variant summary

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

The ENST00000642100.1(CASC19):n.418-33538G>T 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 0.157 in 152,144 control chromosomes in the GnomAD database, including 4,294 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 0.16 ( 4294 hom., cov: 32)

Consequence

CASC19
ENST00000642100.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.805
Variant links:
Genes affected
CASC19 (HGNC:49476): (cancer susceptibility 19)
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CASC19ENST00000642100.1 linkuse as main transcriptn.418-33538G>T intron_variant, non_coding_transcript_variant
PCAT1ENST00000645463.1 linkuse as main transcriptn.855+106053C>A intron_variant, non_coding_transcript_variant
PCAT1ENST00000646670.1 linkuse as main transcriptn.1064+98897C>A intron_variant, non_coding_transcript_variant
PCAT1ENST00000647190.2 linkuse as main transcriptn.1191+63371C>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.157
AC:
23857
AN:
152026
Hom.:
4275
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.434
Gnomad AMI
AF:
0.00219
Gnomad AMR
AF:
0.0684
Gnomad ASJ
AF:
0.0389
Gnomad EAS
AF:
0.244
Gnomad SAS
AF:
0.101
Gnomad FIN
AF:
0.0507
Gnomad MID
AF:
0.0506
Gnomad NFE
AF:
0.0322
Gnomad OTH
AF:
0.112
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.157
AC:
23926
AN:
152144
Hom.:
4294
Cov.:
32
AF XY:
0.155
AC XY:
11508
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.434
Gnomad4 AMR
AF:
0.0683
Gnomad4 ASJ
AF:
0.0389
Gnomad4 EAS
AF:
0.244
Gnomad4 SAS
AF:
0.102
Gnomad4 FIN
AF:
0.0507
Gnomad4 NFE
AF:
0.0322
Gnomad4 OTH
AF:
0.112
Alfa
AF:
0.0660
Hom.:
1086
Bravo
AF:
0.170
Asia WGS
AF:
0.146
AC:
508
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
Cadd
Benign
0.13
Dann
Benign
0.21

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.

Other links and lift over

dbSNP: rs16901979; hg19: chr8-128124916; API