rs2876143

Variant names:

• chr6-8983391-A-G
• rs2876143
• ENST00000642760.1:n.924-8774A>G

Variant summary

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

The ENST00000642760.1(HULC):​n.924-8774A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,990 control chromosomes in the GnomAD database, including 6,654 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 0.26 (6654 hom., cov: 32)
• Consequence: HULC ENST00000642760.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.871
• Publications: 6 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]

LOC105374914 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642760.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HULC	ENST00000642760.1		n.924-8774A>G		intron	N/A
	HULC	ENST00000642798.1		n.691-8774A>G		intron	N/A
	HULC	ENST00000643431.1		n.1149-2339A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40203 AN: 151872 Hom.: 6644 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.265 AC: 40245 AN: 151990 Hom.: 6654 Cov.: 32 AF XY: 0.260 AC XY: 19327 AN XY: 74292

African (AFR) AF: 0.470 AC: 19463 AN: 41426

American (AMR) AF: 0.211 AC: 3225 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3466

East Asian (EAS) AF: 0.186 AC: 957 AN: 5156

South Asian (SAS) AF: 0.115 AC: 556 AN: 4818

European-Finnish (FIN) AF: 0.144 AC: 1523 AN: 10576

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13050 AN: 67964

Other (OTH) AF: 0.245 AC: 517 AN: 2110

Alfa AF: 0.308 Hom.: 3698

Bravo AF: 0.284

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.44
DANN	Benign	0.44
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs2876143; hg19: chr6-8983624;