rs1328868

Variant names:

• chr6-8652345-C-T
• rs1328868
• ENST00000503668.3:n.77C>T

Variant summary

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

The ENST00000503668.3(HULC):​n.77C>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 ENST00000503668.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 4 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=-0.88).
• 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 rank	MANE	Protein	UniProt
HULC	NR_004855.3	n.77C>T		non_coding_transcript_exon_variant	Exon 1 of 2	ENST00000503668.3
LOC100506207	NR_038979.1	n.685-58264C>T		intron_variant	Intron 3 of 3
LOC100506207	NR_038980.1	n.707+93702C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HULC	ENST00000503668.3	n.77C>T		non_coding_transcript_exon_variant	Exon 1 of 2	1	NR_004855.3

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

African (AFR) AF: 0.167 AC: 1 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.400 AC: 12 AN: 30

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.343 AC: 37 AN: 108

Other (OTH) AF: 0.00 AC: 0 AN: 6

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

African (AFR) AF: 0.304 AC: 12594 AN: 41450

American (AMR) AF: 0.363 AC: 5542 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1115 AN: 3472

East Asian (EAS) AF: 0.336 AC: 1730 AN: 5156

South Asian (SAS) AF: 0.272 AC: 1310 AN: 4810

European-Finnish (FIN) AF: 0.464 AC: 4895 AN: 10540

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26225 AN: 67958

Other (OTH) AF: 0.372 AC: 786 AN: 2114

Alfa AF: 0.369 Hom.: 7111

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs1328868; hg19: chr6-8652578;