ENST00000520572.3:n.336-8716C>T

Variant names:

• chr8-142717134-G-A
• rs6471590
• ENST00000520572.3:n.336-8716C>T

Variant summary

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

The ENST00000520572.3(LNCOC1):​n.336-8716C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,156 control chromosomes in the GnomAD database, including 48,617 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 (48617 hom., cov: 32)
• Consequence: LNCOC1 ENST00000520572.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630
• Publications: 6 publications found

Genes affected

LNCOC1 (HGNC:53947): (lncRNA associated with ovarian cancer 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520572.3. 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
	LNCOC1	NR_038925.1		n.253-8716C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNCOC1	ENST00000520572.3	TSL:1	n.336-8716C>T		intron	N/A
	LNCOC1	ENST00000654797.2		n.416+7524C>T		intron	N/A
	LNCOC1	ENST00000662059.1		n.564+3422C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121287 AN: 152038 Hom.: 48580 Cov.: 32

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.798 AC: 121379 AN: 152156 Hom.: 48617 Cov.: 32 AF XY: 0.796 AC XY: 59188 AN XY: 74398

African (AFR) AF: 0.776 AC: 32204 AN: 41490

American (AMR) AF: 0.822 AC: 12581 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2599 AN: 3472

East Asian (EAS) AF: 0.592 AC: 3063 AN: 5178

South Asian (SAS) AF: 0.710 AC: 3423 AN: 4822

European-Finnish (FIN) AF: 0.819 AC: 8652 AN: 10566

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56176 AN: 68012

Other (OTH) AF: 0.794 AC: 1678 AN: 2114

Alfa AF: 0.808 Hom.: 7195

Bravo AF: 0.796

Asia WGS AF: 0.639 AC: 2226 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.17
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs6471590; hg19: chr8-143798552;