rs6917811

Variant summary

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

The NR_015410.2(CASC15):​n.564-2243C>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 0.202 in 152,022 control chromosomes in the GnomAD database, including 3,665 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 0.20 ( 3665 hom., cov: 32)

Consequence

CASC15
NR_015410.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.473
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]

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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CASC15NR_015410.2 linkuse as main transcriptn.564-2243C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CASC15ENST00000688254.1 linkuse as main transcriptn.550+16706C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.202
AC:
30691
AN:
151904
Hom.:
3659
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.314
Gnomad AMI
AF:
0.240
Gnomad AMR
AF:
0.147
Gnomad ASJ
AF:
0.183
Gnomad EAS
AF:
0.00174
Gnomad SAS
AF:
0.0634
Gnomad FIN
AF:
0.149
Gnomad MID
AF:
0.133
Gnomad NFE
AF:
0.181
Gnomad OTH
AF:
0.178
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.202
AC:
30719
AN:
152022
Hom.:
3665
Cov.:
32
AF XY:
0.194
AC XY:
14444
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.314
Gnomad4 AMR
AF:
0.147
Gnomad4 ASJ
AF:
0.183
Gnomad4 EAS
AF:
0.00174
Gnomad4 SAS
AF:
0.0635
Gnomad4 FIN
AF:
0.149
Gnomad4 NFE
AF:
0.181
Gnomad4 OTH
AF:
0.176
Alfa
AF:
0.198
Hom.:
458
Bravo
AF:
0.209
Asia WGS
AF:
0.0460
AC:
161
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
3.2
DANN
Benign
0.63

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: rs6917811; hg19: chr6-21800645; API