6-8849042-A-G

Variant names:

• chr6-8849042-A-G
• rs9393068
• ENST00000642357.1:n.726+12468A>G

Variant summary

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

The ENST00000642357.1(HULC):​n.726+12468A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 152,008 control chromosomes in the GnomAD database, including 22,389 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 0.54 (22389 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: HULC ENST00000642357.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948
• Publications: 2 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642357.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HULC	ENST00000642357.1		n.726+12468A>G		intron	N/A
	HULC	ENST00000642760.1		n.658+12468A>G		intron	N/A
	HULC	ENST00000642798.1		n.690+12468A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81523 AN: 151888 Hom.: 22341 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.540

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.537 AC: 81630 AN: 152008 Hom.: 22389 Cov.: 32 AF XY: 0.541 AC XY: 40221 AN XY: 74280

African (AFR) AF: 0.602 AC: 24940 AN: 41442

American (AMR) AF: 0.597 AC: 9117 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2055 AN: 3466

East Asian (EAS) AF: 0.518 AC: 2672 AN: 5158

South Asian (SAS) AF: 0.655 AC: 3156 AN: 4816

European-Finnish (FIN) AF: 0.565 AC: 5955 AN: 10544

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32084 AN: 67988

Other (OTH) AF: 0.544 AC: 1148 AN: 2112

Alfa AF: 0.484 Hom.: 8373

Bravo AF: 0.545

Asia WGS AF: 0.643 AC: 2235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.35
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs9393068; hg19: chr6-8849275;