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GeneBe

rs10484722

Variant summary

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

The XR_001744024.2(LOC105374971):n.482+2720A>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 0.11 in 152,154 control chromosomes in the GnomAD database, including 1,806 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 0.11 ( 1806 hom., cov: 32)

Consequence

LOC105374971
XR_001744024.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.800
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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105374971XR_001744024.2 linkuse as main transcriptn.482+2720A>G intron_variant, non_coding_transcript_variant
LOC105374971XR_001744025.1 linkuse as main transcriptn.402+2720A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CASC15ENST00000652081.1 linkuse as main transcriptn.145+50712A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.110
AC:
16671
AN:
152036
Hom.:
1800
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.285
Gnomad AMI
AF:
0.124
Gnomad AMR
AF:
0.0574
Gnomad ASJ
AF:
0.0476
Gnomad EAS
AF:
0.00250
Gnomad SAS
AF:
0.0549
Gnomad FIN
AF:
0.0145
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.0451
Gnomad OTH
AF:
0.0970
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.110
AC:
16697
AN:
152154
Hom.:
1806
Cov.:
32
AF XY:
0.106
AC XY:
7886
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.285
Gnomad4 AMR
AF:
0.0572
Gnomad4 ASJ
AF:
0.0476
Gnomad4 EAS
AF:
0.00251
Gnomad4 SAS
AF:
0.0544
Gnomad4 FIN
AF:
0.0145
Gnomad4 NFE
AF:
0.0451
Gnomad4 OTH
AF:
0.0960
Alfa
AF:
0.0571
Hom.:
568
Bravo
AF:
0.122
Asia WGS
AF:
0.0420
AC:
148
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
0.57
Dann
Benign
0.41

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: rs10484722; hg19: chr6-22403592; API