rs4712652

Variant names:

• chr6-22078386-G-A
• rs4712652
• ENST00000444265.6:n.887+15146G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-22078386-G-A
• chr6-22078386-G-C
• chr6-22078386-G-T

Variant summary

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

The ENST00000444265.6(CASC15):​n.887+15146G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,818 control chromosomes in the GnomAD database, including 31,737 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 0.64 (31737 hom., cov: 31)
• Consequence: CASC15 ENST00000444265.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.75

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC15	NR_015410.2	n.1248+21696G>A		intron_variant	Intron 8 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000444265.6	n.887+15146G>A		intron_variant	Intron 6 of 10	1
CASC15	ENST00000606851.5	n.1217+21696G>A		intron_variant	Intron 8 of 11	2
CASC15	ENST00000607048.5	n.843+21696G>A		intron_variant	Intron 7 of 11	2

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97314 AN: 151698 Hom.: 31710 Cov.: 31

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.641 AC: 97391 AN: 151818 Hom.: 31737 Cov.: 31 AF XY: 0.647 AC XY: 48012 AN XY: 74180

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.861

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.592

Alfa AF: 0.582 Hom.: 9981

Bravo AF: 0.642

Asia WGS AF: 0.688 AC: 2389 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.019
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4712652; hg19: chr6-22078615;