rs6916371

Variant names:

• chr6-22151856-A-G
• rs6916371
• ENST00000444265.6:n.1062-39711A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-22151856-A-G
• chr6-22151856-A-T

Variant summary

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

The ENST00000444265.6(CASC15):​n.1062-39711A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.926 in 152,208 control chromosomes in the GnomAD database, including 65,802 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 0.93 (65802 hom., cov: 32)
• Consequence: CASC15 ENST00000444265.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.982
• Publications: 0 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.964 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.1423-22142A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC15	ENST00000444265.6	TSL:1	n.1062-39711A>G		intron	N/A
	CASC15	ENST00000561912.3	TSL:5	n.199+4786A>G		intron	N/A
	CASC15	ENST00000567753.2	TSL:6	n.88+4786A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.926 AC: 140888 AN: 152090 Hom.: 65767 Cov.: 32

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.971

Gnomad OTH AF: 0.937

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

GnomAD4 genome AF: 0.926 AC: 140974 AN: 152208 Hom.: 65802 Cov.: 32 AF XY: 0.922 AC XY: 68612 AN XY: 74410

African (AFR) AF: 0.907 AC: 37664 AN: 41542

American (AMR) AF: 0.838 AC: 12801 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.978 AC: 3395 AN: 3472

East Asian (EAS) AF: 0.595 AC: 3077 AN: 5170

South Asian (SAS) AF: 0.963 AC: 4646 AN: 4826

European-Finnish (FIN) AF: 0.964 AC: 10208 AN: 10586

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.971 AC: 66006 AN: 68010

Other (OTH) AF: 0.938 AC: 1981 AN: 2112

Alfa AF: 0.960 Hom.: 8827

Bravo AF: 0.913

Asia WGS AF: 0.816 AC: 2828 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.8
DANN	Benign	0.60
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs6916371; hg19: chr6-22152085;