rs6911727

Variant names:

• chr6-9116165-T-C
• rs6911727
• ENST00000642760.1:n.1125+69674T>C

Variant summary

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

The ENST00000642760.1(HULC):​n.1125+69674T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 152,078 control chromosomes in the GnomAD database, including 20,565 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 0.49 (20565 hom., cov: 32)
• Consequence: HULC ENST00000642760.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171
• Publications: 11 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=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HULC	ENST00000642760.1	n.1125+69674T>C		intron_variant	Intron 7 of 9
HULC	ENST00000642798.1	n.892+69674T>C		intron_variant	Intron 5 of 6
HULC	ENST00000643788.1	n.969+69674T>C		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74332 AN: 151960 Hom.: 20520 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.489 AC: 74429 AN: 152078 Hom.: 20565 Cov.: 32 AF XY: 0.482 AC XY: 35821 AN XY: 74342

African (AFR) AF: 0.762 AC: 31620 AN: 41478

American (AMR) AF: 0.354 AC: 5418 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1431 AN: 3472

East Asian (EAS) AF: 0.522 AC: 2696 AN: 5160

South Asian (SAS) AF: 0.378 AC: 1821 AN: 4822

European-Finnish (FIN) AF: 0.323 AC: 3412 AN: 10562

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26500 AN: 67982

Other (OTH) AF: 0.470 AC: 991 AN: 2110

Alfa AF: 0.405 Hom.: 7359

Bravo AF: 0.506

Asia WGS AF: 0.468 AC: 1633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	0.58
DANN	Benign	0.67
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6911727; hg19: chr6-9116398;