Genetic Variant HULC:n.122+64A>G (chr6-8652454-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000503668.3(HULC):n.122+64A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 152,150 control chromosomes in the GnomAD database, including 15,059 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 0.44 ( 15053 hom., cov: 32)

Exomes 𝑓: 0.38 ( 6 hom. )

Consequence

HULC
ENST00000503668.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20

Publications

4 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE
HULC	NR_004855.3 link	n.122+64A>G	intron_variant	Intron 1 of 1	ENST00000503668.3
LOC100506207	NR_038979.1 link	n.685-58155A>G	intron_variant	Intron 3 of 3
LOC100506207	NR_038980.1 link	n.707+93811A>G	intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HULC	ENST00000503668.3 link	n.122+64A>G		intron_variant	Intron 1 of 1	1	NR_004855.3

Frequencies

GnomAD3 genomes

AF:

0.440

AC:

66875

AN:

151954

Hom.:

15048

Cov.:

show subpopulations

Gnomad AFR

AF:

0.397

Gnomad AMI

AF:

0.361

Gnomad AMR

AF:

0.443

Gnomad ASJ

AF:

0.408

Gnomad EAS

AF:

0.430

Gnomad SAS

AF:

0.350

Gnomad FIN

AF:

0.548

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.458

Gnomad OTH

AF:

0.460

GnomAD4 exome

AF:

0.375

AC:

AN:

Hom.:

Cov.:

AF XY:

0.375

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.167

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.419

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.564

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.440

AC:

66919

AN:

152070

Hom.:

15053

Cov.:

AF XY:

0.444

AC XY:

32987

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.396

AC:

16443

AN:

41472

American (AMR)

AF:

0.443

AC:

6762

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.408

AC:

1415

AN:

3472

East Asian (EAS)

AF:

0.430

AC:

2221

AN:

5162

South Asian (SAS)

AF:

0.349

AC:

1682

AN:

4822

European-Finnish (FIN)

AF:

0.548

AC:

5798

AN:

10578

Middle Eastern (MID)

AF:

0.429

AC:

126

AN:

294

European-Non Finnish (NFE)

AF:

0.458

AC:

31165

AN:

67972

Other (OTH)

AF:

0.463

AC:

978

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1907

3815

5722

7630

9537

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

624

1248

1872

2496

3120

<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:

0.450

Hom.:

2013

Bravo

AF:

0.432

Asia WGS

AF:

0.417

AC:

1450

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.3

(source)

DANN

Benign

0.28

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over