ENST00000444265.6:n.1061+39209G>A

Variant names:

• chr6-22150129-G-A
• rs10498705
• ENST00000444265.6:n.1061+39209G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000444265.6(CASC15):​n.1061+39209G>A variant causes a intron change. The variant allele was found at a frequency of 0.106 in 152,138 control chromosomes in the GnomAD database, including 1,110 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 0.11 (1110 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: CASC15 ENST00000444265.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.28
• Publications: 2 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC15	NR_015410.2	n.1423-23869G>A		intron_variant	Intron 9 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000444265.6	n.1061+39209G>A		intron_variant	Intron 7 of 10	1
CASC15	ENST00000605917.2	n.3861G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
CASC15	ENST00000561912.3	n.199+3059G>A		intron_variant	Intron 1 of 10	5

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16202 AN: 152018 Hom.: 1114 Cov.: 32

Gnomad AFR AF: 0.0403

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0794

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.00597

Gnomad SAS AF: 0.0990

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.0986

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.106 AC: 16187 AN: 152136 Hom.: 1110 Cov.: 32 AF XY: 0.106 AC XY: 7913 AN XY: 74380

African (AFR) AF: 0.0401 AC: 1666 AN: 41536

American (AMR) AF: 0.0793 AC: 1212 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3470

East Asian (EAS) AF: 0.00598 AC: 31 AN: 5180

South Asian (SAS) AF: 0.0977 AC: 469 AN: 4802

European-Finnish (FIN) AF: 0.186 AC: 1962 AN: 10564

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10118 AN: 67980

Other (OTH) AF: 0.0961 AC: 203 AN: 2112

Alfa AF: 0.132 Hom.: 3099

Bravo AF: 0.0948

Asia WGS AF: 0.0470 AC: 167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	22
DANN	Benign	0.83
PhyloP100		4.3

Splicing

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

Other links and lift over

dbSNP: rs10498705; hg19: chr6-22150358;