rs6937402

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000561912.3(CASC15):​n.200-32225T>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 0.0552 in 152,288 control chromosomes in the GnomAD database, including 238 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 0.055 ( 238 hom., cov: 33)

Consequence

CASC15
ENST00000561912.3 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.768
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 -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.26).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0597 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.200-32225T>G intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.0552
AC:
8397
AN:
152170
Hom.:
238
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0533
Gnomad AMI
AF:
0.162
Gnomad AMR
AF:
0.0368
Gnomad ASJ
AF:
0.0216
Gnomad EAS
AF:
0.00212
Gnomad SAS
AF:
0.0385
Gnomad FIN
AF:
0.0857
Gnomad MID
AF:
0.0285
Gnomad NFE
AF:
0.0612
Gnomad OTH
AF:
0.0589
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0552
AC:
8403
AN:
152288
Hom.:
238
Cov.:
33
AF XY:
0.0553
AC XY:
4121
AN XY:
74464
show subpopulations
Gnomad4 AFR
AF:
0.0532
Gnomad4 AMR
AF:
0.0367
Gnomad4 ASJ
AF:
0.0216
Gnomad4 EAS
AF:
0.00212
Gnomad4 SAS
AF:
0.0387
Gnomad4 FIN
AF:
0.0857
Gnomad4 NFE
AF:
0.0612
Gnomad4 OTH
AF:
0.0587
Alfa
AF:
0.0568
Hom.:
330
Bravo
AF:
0.0513
Asia WGS
AF:
0.0220
AC:
75
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.26
CADD
Benign
15
DANN
Benign
0.83

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: rs6937402; hg19: chr6-22224378; API