6-22060353-T-C

Position:

• chr6-22060353-T-C

Variant summary

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

The NR_015410.2(CASC15):​n.1248+3663T>C 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 0.71 in 152,076 control chromosomes in the GnomAD database, including 38,999 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 0.71 (38999 hom., cov: 32)
• Consequence: CASC15 NR_015410.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820

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 = 0.883 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC15	NR_015410.2	n.1248+3663T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC15	ENST00000688254.1	n.1151+3663T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107853 AN: 151958 Hom.: 38965 Cov.: 32

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.710 AC: 107938 AN: 152076 Hom.: 38999 Cov.: 32 AF XY: 0.716 AC XY: 53163 AN XY: 74298

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.740

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.659

Alfa AF: 0.652 Hom.: 16284

Bravo AF: 0.714

Asia WGS AF: 0.728 AC: 2535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs885769; hg19: chr6-22060582;