6-22306471-A-G

Position:

• chr6-22306471-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000561912.3(CASC15):​n.570-10356A>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 0.614 in 152,058 control chromosomes in the GnomAD database, including 28,637 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 0.61 (28637 hom., cov: 33)
• Consequence: CASC15 ENST00000561912.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000561912.3	n.570-10356A>G		intron_variant, non_coding_transcript_variant		5
CASC15	ENST00000651569.1	n.506-10356A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93270 AN: 151938 Hom.: 28597 Cov.: 33

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.624

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.614 AC: 93366 AN: 152058 Hom.: 28637 Cov.: 33 AF XY: 0.616 AC XY: 45747 AN XY: 74310

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.783

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.627

Alfa AF: 0.597 Hom.: 3392

Bravo AF: 0.618

Asia WGS AF: 0.666 AC: 2304 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.32
DANN	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1341238; hg19: chr6-22306700;