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GeneBe

rs6983561

Variant summary

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

The ENST00000642100.1(CASC19):n.418-15502T>G 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 0.164 in 152,164 control chromosomes in the GnomAD database, including 4,774 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. There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.16 ( 4774 hom., cov: 32)

Consequence

CASC19
ENST00000642100.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.738
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=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 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.418-15502T>G intron_variant, non_coding_transcript_variant
PCAT1ENST00000645463.1 linkuse as main transcriptn.855+88017A>C intron_variant, non_coding_transcript_variant
PCAT1ENST00000646670.1 linkuse as main transcriptn.1064+80861A>C intron_variant, non_coding_transcript_variant
PCAT1ENST00000647190.2 linkuse as main transcriptn.1191+45335A>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.164
AC:
24873
AN:
152046
Hom.:
4758
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.458
Gnomad AMI
AF:
0.00219
Gnomad AMR
AF:
0.0703
Gnomad ASJ
AF:
0.0389
Gnomad EAS
AF:
0.244
Gnomad SAS
AF:
0.101
Gnomad FIN
AF:
0.0509
Gnomad MID
AF:
0.0475
Gnomad NFE
AF:
0.0324
Gnomad OTH
AF:
0.116
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.164
AC:
24938
AN:
152164
Hom.:
4774
Cov.:
32
AF XY:
0.161
AC XY:
11976
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.458
Gnomad4 AMR
AF:
0.0702
Gnomad4 ASJ
AF:
0.0389
Gnomad4 EAS
AF:
0.244
Gnomad4 SAS
AF:
0.102
Gnomad4 FIN
AF:
0.0509
Gnomad4 NFE
AF:
0.0324
Gnomad4 OTH
AF:
0.117
Alfa
AF:
0.0539
Hom.:
1292
Bravo
AF:
0.178
Asia WGS
AF:
0.145
AC:
505
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.2
DANN
Benign
0.40

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: rs6983561; hg19: chr8-128106880; API