6-8582699-A-T

Variant names:

• chr6-8582699-A-T
• rs850157
• ENST00000642163.1:n.700+24056A>T

Variant summary

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

The ENST00000642163.1(HULC):​n.700+24056A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,820 control chromosomes in the GnomAD database, including 6,479 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 0.29 (6479 hom., cov: 30)
• Consequence: HULC ENST00000642163.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.58
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100506207	NR_038979.1	n.684+24056A>T		intron_variant	Intron 3 of 3
LOC100506207	NR_038980.1	n.707+24056A>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HULC	ENST00000642163.1	n.700+24056A>T		intron_variant	Intron 4 of 7
HULC	ENST00000642168.1	n.797+24056A>T		intron_variant	Intron 4 of 4
HULC	ENST00000642340.2	n.659+24056A>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44068 AN: 151702 Hom.: 6482 Cov.: 30

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.290 AC: 44080 AN: 151820 Hom.: 6479 Cov.: 30 AF XY: 0.290 AC XY: 21524 AN XY: 74178

African (AFR) AF: 0.276 AC: 11435 AN: 41380

American (AMR) AF: 0.284 AC: 4319 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1119 AN: 3468

East Asian (EAS) AF: 0.266 AC: 1373 AN: 5152

South Asian (SAS) AF: 0.413 AC: 1988 AN: 4810

European-Finnish (FIN) AF: 0.283 AC: 2981 AN: 10548

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19939 AN: 67932

Other (OTH) AF: 0.297 AC: 626 AN: 2108

Alfa AF: 0.290 Hom.: 760

Bravo AF: 0.288

Asia WGS AF: 0.324 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.2
DANN	Benign	0.47
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs850157; hg19: chr6-8582932;