rs1047953

Variant names:

• chr6-22186635-G-A
• rs1047953
• ENST00000444265.6:n.1062-4932G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-22186635-G-A
• chr6-22186635-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000444265.6(CASC15):​n.1062-4932G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 152,034 control chromosomes in the GnomAD database, including 36,176 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 0.67 (36176 hom., cov: 32)
• Consequence: CASC15 ENST00000444265.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734
• Publications: 4 publications found

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]

NBAT1 (HGNC:49075): (neuroblastoma associated transcript 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444265.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC15	NR_015410.2		n.1488-4932G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC15	ENST00000444265.6	TSL:1	n.1062-4932G>A		intron	N/A
	CASC15	ENST00000561912.3	TSL:5	n.199+39565G>A		intron	N/A
	CASC15	ENST00000567753.2	TSL:6	n.89-27672G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101546 AN: 151916 Hom.: 36169 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.668 AC: 101583 AN: 152034 Hom.: 36176 Cov.: 32 AF XY: 0.672 AC XY: 49989 AN XY: 74344

African (AFR) AF: 0.404 AC: 16718 AN: 41404

American (AMR) AF: 0.750 AC: 11465 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2399 AN: 3472

East Asian (EAS) AF: 0.831 AC: 4305 AN: 5180

South Asian (SAS) AF: 0.627 AC: 3023 AN: 4818

European-Finnish (FIN) AF: 0.848 AC: 8973 AN: 10580

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52615 AN: 67970

Other (OTH) AF: 0.664 AC: 1402 AN: 2110

Alfa AF: 0.733 Hom.: 31439

Bravo AF: 0.652

Asia WGS AF: 0.697 AC: 2426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.33
DANN	Benign	0.70
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs1047953; hg19: chr6-22186864;