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GeneBe

rs9358531

Variant summary

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

The ENST00000561912.3(CASC15):n.570-7426T>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 0.328 in 152,002 control chromosomes in the GnomAD database, including 9,517 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 0.33 ( 9517 hom., cov: 31)

Consequence

CASC15
ENST00000561912.3 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0460
Variant links:
Genes affected
CASC15 (HGNC:28245): (cancer susceptibility 15) This gene produces a long non-coding RNA that may regulate cell proliferation. This RNA is upregulated in hepatocellular carcinoma, where it is thought to function as an oncogene. However, some splice variants of this gene may function as a tumor suppressor in neuroblastoma and other tumor types. Circular RNA variants were observed at this gene. [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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.422 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
CASC15ENST00000561912.3 linkuse as main transcriptn.570-7426T>G intron_variant, non_coding_transcript_variant 5
CASC15ENST00000651569.1 linkuse as main transcriptn.506-7426T>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.328
AC:
49848
AN:
151884
Hom.:
9521
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.136
Gnomad AMI
AF:
0.358
Gnomad AMR
AF:
0.339
Gnomad ASJ
AF:
0.424
Gnomad EAS
AF:
0.383
Gnomad SAS
AF:
0.272
Gnomad FIN
AF:
0.393
Gnomad MID
AF:
0.411
Gnomad NFE
AF:
0.426
Gnomad OTH
AF:
0.369
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.328
AC:
49853
AN:
152002
Hom.:
9517
Cov.:
31
AF XY:
0.328
AC XY:
24371
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.136
Gnomad4 AMR
AF:
0.339
Gnomad4 ASJ
AF:
0.424
Gnomad4 EAS
AF:
0.383
Gnomad4 SAS
AF:
0.273
Gnomad4 FIN
AF:
0.393
Gnomad4 NFE
AF:
0.426
Gnomad4 OTH
AF:
0.369
Alfa
AF:
0.364
Hom.:
2398
Bravo
AF:
0.317
Asia WGS
AF:
0.288
AC:
1002
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
Cadd
Benign
2.0
Dann
Benign
0.74

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: rs9358531; hg19: chr6-22309630; API