Genetic Variant HULC:n.122+48C>G (chr6-8652438-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000646741.1(HULC):n.177C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,286 control chromosomes in the GnomAD database, including 3,159 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 0.18 ( 3158 hom., cov: 33)

Exomes 𝑓: 0.21 ( 1 hom. )

Consequence

HULC
ENST00000646741.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.16

Publications

7 publications found

Variant links:

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]

HULC links:

ENSG00000285216 (HGNC:):

ENSG00000285216 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646741.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
HULC	NR_004855.3	MANE Select	n.122+48C>G	intron	N/A
LOC100506207	NR_038979.1		n.685-58171C>G	intron	N/A
LOC100506207	NR_038980.1		n.707+93795C>G	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
HULC	ENST00000503668.3	TSL:1 MANE Select	n.122+48C>G	intron	N/A
HULC	ENST00000646741.1		n.177C>G	non_coding_transcript_exon	Exon 1 of 2
HULC	ENST00000665267.1		n.177C>G	non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.182

AC:

27738

AN:

152064

Hom.:

3158

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0470

Gnomad AMI

AF:

0.416

Gnomad AMR

AF:

0.241

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.251

Gnomad SAS

AF:

0.212

Gnomad FIN

AF:

0.139

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.245

Gnomad OTH

AF:

0.178

GnomAD4 exome

AF:

0.212

AC:

AN:

104

Hom.:

Cov.:

AF XY:

0.209

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.333

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.182

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.182

AC:

27742

AN:

152182

Hom.:

3158

Cov.:

AF XY:

0.180

AC XY:

13402

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.0468

AC:

1945

AN:

41534

American (AMR)

AF:

0.241

AC:

3686

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

865

AN:

3466

East Asian (EAS)

AF:

0.251

AC:

1299

AN:

5174

South Asian (SAS)

AF:

0.213

AC:

1028

AN:

4818

European-Finnish (FIN)

AF:

0.139

AC:

1473

AN:

10594

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.245

AC:

16631

AN:

67994

Other (OTH)

AF:

0.176

AC:

373

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1110

2220

3331

4441

5551

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

306

612

918

1224

1530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0988

Hom.:

156

Bravo

AF:

0.183

Asia WGS

AF:

0.203

AC:

707

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.16

(source)

DANN

Benign

0.66

PhyloP100

-1.2

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over