rs1935007

Positions:

• chr6-22343072-A-G

Variant summary

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

The ENST00000561912.3(CASC15):​n.800-475A>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 0.29 in 152,106 control chromosomes in the GnomAD database, including 7,834 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 0.29 (7834 hom., cov: 33)
• Consequence: CASC15 ENST00000561912.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 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
CASC15	ENST00000561912.3	n.800-475A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44077 AN: 151988 Hom.: 7834 Cov.: 33

Gnomad AFR AF: 0.0774

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.290 AC: 44090 AN: 152106 Hom.: 7834 Cov.: 33 AF XY: 0.293 AC XY: 21773 AN XY: 74314

Gnomad4 AFR AF: 0.0772

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.297

Alfa AF: 0.370 Hom.: 21457

Bravo AF: 0.274

Asia WGS AF: 0.270 AC: 939 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1935007; hg19: chr6-22343301;