6-8653014-A-G

Variant names:

• chr6-8653014-A-G
• rs7763881
• ENST00000503668.2:n.255-531A>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000646741.1(HULC):​n.753A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: HULC ENST00000646741.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HULC	NR_004855.3	n.123-531A>G		intron_variant	Intron 1 of 1
LOC100506207	NR_038979.1	n.685-57595A>G		intron_variant	Intron 3 of 3
LOC100506207	NR_038980.1	n.707+94371A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HULC	ENST00000503668.2	n.255-531A>G		intron_variant	Intron 1 of 1	1
HULC	ENST00000646741.1	n.753A>G		non_coding_transcript_exon_variant	Exon 1 of 2
HULC	ENST00000665267.1	n.753A>G		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.19
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7763881; hg19: chr6-8653247;