rs6911727

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.470

Alfa AF: 0.405 Hom.: 6712

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6911727; hg19: chr6-9116398;