ENST00000642163.1:n.544-21990T>C

Variant names:

• chr6-8525127-T-C
• rs1410766
• ENST00000642163.1:n.544-21990T>C

Variant summary

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

The ENST00000642163.1(HULC):​n.544-21990T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,040 control chromosomes in the GnomAD database, including 28,620 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 0.61 (28620 hom., cov: 32)
• Consequence: HULC ENST00000642163.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100506207	NR_038979.1	n.626-33458T>C		intron_variant	Intron 2 of 3
LOC100506207	NR_038980.1	n.649-33458T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HULC	ENST00000642163.1	n.544-21990T>C		intron_variant	Intron 2 of 7
HULC	ENST00000642168.1	n.641-21990T>C		intron_variant	Intron 2 of 4
HULC	ENST00000642340.1	n.601-33458T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92292 AN: 151922 Hom.: 28599 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.608 AC: 92365 AN: 152040 Hom.: 28620 Cov.: 32 AF XY: 0.618 AC XY: 45945 AN XY: 74318

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.847

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.740

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.646

Alfa AF: 0.500 Hom.: 1565

Bravo AF: 0.602

Asia WGS AF: 0.714 AC: 2481 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	0.45
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1410766; hg19: chr6-8525360;