rs1328866

chr6-8653283-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_004855.2(HULC):n.183-262T>A variant causes a intron, non coding transcript 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 NR_004855.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127

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]

LOC100506207 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HULC	NR_004855.2	n.183-262T>A		intron_variant, non_coding_transcript_variant
LOC100506207	NR_038980.1	n.707+94640T>A		intron_variant, non_coding_transcript_variant
LOC100506207	NR_038979.1	n.685-57326T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HULC	ENST00000645747.1	n.313+106069T>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.501

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	8.3
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

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