ENST00000503668.3:n.123-262T>A

Variant names:

• chr6-8653283-T-A
• rs1328866
• ENST00000503668.3:n.123-262T>A

Variant summary

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

The ENST00000503668.3(HULC):​n.123-262T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,944 control chromosomes in the GnomAD database, including 18,070 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 0.48 (18070 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: HULC ENST00000503668.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 1 publications found

Genes affected

HULC (HGNC:34232): (hepatocellular carcinoma up-regulated long non-coding RNA) This gene produces a long RNA that was discovered as upregulated in hepatocellular carcinoma and is associated with cancer progression. Expression of this transcript is regulated by microRNAs and at the transcriptional level by Sp1 family factors. The transcript may regulate gene expression by functioning as a competing RNA for microRNAs. [provided by RefSeq, Dec 2017]

ENSG00000285216 (HGNC:):

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 = 0.52 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503668.3. 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
	HULC	NR_004855.3	MANE Select	n.123-262T>A		intron	N/A
	LOC100506207	NR_038979.1		n.685-57326T>A		intron	N/A
	LOC100506207	NR_038980.1		n.707+94640T>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HULC	ENST00000503668.3	TSL:1 MANE Select	n.123-262T>A		intron	N/A
	HULC	ENST00000642163.1		n.700+94640T>A		intron	N/A
	HULC	ENST00000642168.1		n.798-262T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73390 AN: 151826 Hom.: 18064 Cov.: 31

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.483 AC: 73442 AN: 151944 Hom.: 18070 Cov.: 31 AF XY: 0.487 AC XY: 36179 AN XY: 74234

African (AFR) AF: 0.526 AC: 21779 AN: 41424

American (AMR) AF: 0.460 AC: 7027 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1436 AN: 3466

East Asian (EAS) AF: 0.481 AC: 2479 AN: 5154

South Asian (SAS) AF: 0.371 AC: 1785 AN: 4812

European-Finnish (FIN) AF: 0.578 AC: 6089 AN: 10538

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31335 AN: 67962

Other (OTH) AF: 0.501 AC: 1056 AN: 2108

Alfa AF: 0.481 Hom.: 2193

Bravo AF: 0.480

Asia WGS AF: 0.459 AC: 1596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	8.3
DANN	Benign	0.61
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs1328866; hg19: chr6-8653516; COSMIC: COSV72247482;