rs1328867

Positions:

• chr6-8652454-A-G

Variant summary

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

The NR_004855.2(HULC):​n.182+64A>G 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 0.44 in 152,150 control chromosomes in the GnomAD database, including 15,059 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 0.44 (15053 hom., cov: 32)
  • Exomes 𝑓: 0.38 (6 hom.)
• Consequence: HULC NR_004855.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HULC	NR_004855.2	n.182+64A>G		intron_variant, non_coding_transcript_variant
LOC100506207	NR_038980.1	n.707+93811A>G		intron_variant, non_coding_transcript_variant
LOC100506207	NR_038979.1	n.685-58155A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HULC	ENST00000645747.1	n.313+105240A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66875 AN: 151954 Hom.: 15048 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.460

GnomAD4 exome AF: 0.375 AC: 30 AN: 80 Hom.: 6 Cov.: 0 AF XY: 0.375 AC XY: 24 AN XY: 64

Gnomad4 AFR exome AF: 0.167

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.419

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.440 AC: 66919 AN: 152070 Hom.: 15053 Cov.: 32 AF XY: 0.444 AC XY: 32987 AN XY: 74342

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.463

Alfa AF: 0.453 Hom.: 1949

Bravo AF: 0.432

Asia WGS AF: 0.417 AC: 1450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1328867; hg19: chr6-8652687;