6-22140212-G-T

Variant names:

• chr6-22140212-G-T
• rs7774801
• ENST00000444265.6:n.1061+29292G>T

Variant summary

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

The ENST00000444265.6(CASC15):​n.1061+29292G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.91 in 152,262 control chromosomes in the GnomAD database, including 63,280 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 0.91 (63280 hom., cov: 33)
• Consequence: CASC15 ENST00000444265.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC15	NR_015410.2	n.1422+29292G>T		intron_variant	Intron 9 of 11
NBAT1	NR_034143.1	n.228-3543C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000444265.6	n.1061+29292G>T		intron_variant	Intron 7 of 10	1
NBAT1	ENST00000566912.2	n.228-3543C>A		intron_variant	Intron 2 of 2	2
CASC15	ENST00000606851.5	n.1391+29292G>T		intron_variant	Intron 9 of 11	2

Frequencies

GnomAD3 genomes AF: 0.911 AC: 138528 AN: 152144 Hom.: 63235 Cov.: 33

Gnomad AFR AF: 0.979

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.910 AC: 138629 AN: 152262 Hom.: 63280 Cov.: 33 AF XY: 0.908 AC XY: 67575 AN XY: 74434

African (AFR) AF: 0.979 AC: 40673 AN: 41550

American (AMR) AF: 0.886 AC: 13547 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.891 AC: 3089 AN: 3468

East Asian (EAS) AF: 0.839 AC: 4341 AN: 5174

South Asian (SAS) AF: 0.856 AC: 4134 AN: 4832

European-Finnish (FIN) AF: 0.906 AC: 9608 AN: 10604

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.887 AC: 60328 AN: 68030

Other (OTH) AF: 0.884 AC: 1868 AN: 2112

Alfa AF: 0.888 Hom.: 95670

Bravo AF: 0.913

Asia WGS AF: 0.839 AC: 2921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.13
DANN	Benign	0.32
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs7774801; hg19: chr6-22140441;