6-8652345-C-T

Position:

• chr6-8652345-C-T

Variant summary

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

The NR_004855.2(HULC):​n.137C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 152,124 control chromosomes in the GnomAD database, including 10,156 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 0.36 (10144 hom., cov: 31)
  • Exomes 𝑓: 0.32 (12 hom.)
• Consequence: HULC NR_004855.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HULC	NR_004855.2	n.137C>T		non_coding_transcript_exon_variant	1/2
LOC100506207	NR_038980.1	n.707+93702C>T		intron_variant, non_coding_transcript_variant
LOC100506207	NR_038979.1	n.685-58264C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HULC	ENST00000645747.1	n.313+105131C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54595 AN: 151852 Hom.: 10145 Cov.: 31

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.373

GnomAD4 exome AF: 0.325 AC: 50 AN: 154 Hom.: 12 Cov.: 0 AF XY: 0.288 AC XY: 30 AN XY: 104

Gnomad4 AFR exome AF: 0.167

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.343

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.359 AC: 54601 AN: 151970 Hom.: 10144 Cov.: 31 AF XY: 0.363 AC XY: 26996 AN XY: 74290

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.372

Alfa AF: 0.366 Hom.: 5032

Bravo AF: 0.350

Asia WGS AF: 0.299 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1328868; hg19: chr6-8652578;