ENST00000821964.1:n.278-5399A>C

Variant names:

• chr6-22660103-T-G
• rs9466427
• ENST00000821964.1:n.278-5399A>C

Variant summary

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

The ENST00000821964.1(LINC03005):​n.278-5399A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.826 in 152,124 control chromosomes in the GnomAD database, including 52,501 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 0.83 (52501 hom., cov: 32)
• Consequence: LINC03005 ENST00000821964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 2 publications found

Genes affected

LINC03005 (HGNC:):

LINC03005 (HGNC:56130): (long intergenic non-protein coding RNA 3005)

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03005	NR_134613.1	n.205-5399A>C		intron_variant	Intron 1 of 1
LINC03005	NR_134614.1	n.249+6892A>C		intron_variant	Intron 2 of 2
LOC105374973	XR_001744026.2	n.*81T>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03005	ENST00000821964.1	n.278-5399A>C		intron_variant	Intron 1 of 1
CASC15	ENST00000822125.1	n.*82T>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125529 AN: 152006 Hom.: 52442 Cov.: 32

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.885

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.826 AC: 125647 AN: 152124 Hom.: 52501 Cov.: 32 AF XY: 0.826 AC XY: 61429 AN XY: 74334

African (AFR) AF: 0.953 AC: 39595 AN: 41536

American (AMR) AF: 0.856 AC: 13083 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2602 AN: 3466

East Asian (EAS) AF: 0.650 AC: 3358 AN: 5164

South Asian (SAS) AF: 0.802 AC: 3867 AN: 4820

European-Finnish (FIN) AF: 0.782 AC: 8259 AN: 10564

Middle Eastern (MID) AF: 0.887 AC: 259 AN: 292

European-Non Finnish (NFE) AF: 0.766 AC: 52073 AN: 67982

Other (OTH) AF: 0.810 AC: 1711 AN: 2112

Alfa AF: 0.806 Hom.: 8339

Bravo AF: 0.839

Asia WGS AF: 0.739 AC: 2572 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.24
DANN	Benign	0.43
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9466427; hg19: chr6-22660332;