6-22655370-T-C

Variant names:

• chr6-22655370-T-C
• rs6905924
• ENST00000821964.1:n.278-666A>G

Variant summary

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

The ENST00000821964.1(LINC03005):​n.278-666A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 152,002 control chromosomes in the GnomAD database, including 48,378 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 0.80 (48378 hom., cov: 31)
• Consequence: LINC03005 ENST00000821964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608
• Publications: 3 publications found

Genes affected

LINC03005 (HGNC:):

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]

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

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 = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821964.1. 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
	LINC03005	NR_134613.1		n.205-666A>G		intron	N/A
	LINC03005	NR_134614.1		n.250-11352A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03005	ENST00000821964.1		n.278-666A>G		intron	N/A
	CASC15	ENST00000822125.1		n.466+338T>C		intron	N/A
	CASC15	ENST00000822127.1		n.181+338T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120788 AN: 151884 Hom.: 48340 Cov.: 31

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.795 AC: 120882 AN: 152002 Hom.: 48378 Cov.: 31 AF XY: 0.796 AC XY: 59106 AN XY: 74280

African (AFR) AF: 0.866 AC: 35908 AN: 41478

American (AMR) AF: 0.846 AC: 12908 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2558 AN: 3468

East Asian (EAS) AF: 0.624 AC: 3228 AN: 5170

South Asian (SAS) AF: 0.760 AC: 3650 AN: 4804

European-Finnish (FIN) AF: 0.781 AC: 8238 AN: 10554

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51641 AN: 67958

Other (OTH) AF: 0.788 AC: 1661 AN: 2108

Alfa AF: 0.765 Hom.: 18140

Bravo AF: 0.806

Asia WGS AF: 0.693 AC: 2415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.81
DANN	Benign	0.71
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs6905924; hg19: chr6-22655599;