dbSNP rs7763881: HULC:n.123-531A>C (chr6-8653014-A-C) – 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.123-531A>C 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 152,044 control chromosomes in the GnomAD database, including 15,029 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 ( 15028 hom., cov: 32)

Exomes 𝑓: 0.38 ( 1 hom. )

Consequence

HULC
ENST00000503668.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.78

Publications

52 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:

Genome browser will be placed here

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=-0.85).

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
HULC	NR_004855.3 link	n.123-531A>C	intron_variant	Intron 1 of 1
LOC100506207	NR_038979.1 link	n.685-57595A>C	intron_variant	Intron 3 of 3
LOC100506207	NR_038980.1 link	n.707+94371A>C	intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HULC	ENST00000503668.3 link	n.123-531A>C	intron_variant	Intron 1 of 1	1
HULC	ENST00000646741.1 link	n.753A>C	non_coding_transcript_exon_variant	Exon 1 of 2
HULC	ENST00000665267.1 link	n.753A>C	non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.440

AC:

66828

AN:

151910

Hom.:

15023

Cov.:

show subpopulations

Gnomad AFR

AF:

0.396

Gnomad AMI

AF:

0.359

Gnomad AMR

AF:

0.443

Gnomad ASJ

AF:

0.409

Gnomad EAS

AF:

0.430

Gnomad SAS

AF:

0.350

Gnomad FIN

AF:

0.549

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.458

Gnomad OTH

AF:

0.460

GnomAD4 exome

AF:

0.375

AC:

AN:

Hom.:

Cov.:

AF XY:

0.429

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.429

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.440

AC:

66871

AN:

152028

Hom.:

15028

Cov.:

AF XY:

0.444

AC XY:

32949

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.396

AC:

16406

AN:

41472

American (AMR)

AF:

0.443

AC:

6763

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.409

AC:

1414

AN:

3460

East Asian (EAS)

AF:

0.430

AC:

2214

AN:

5154

South Asian (SAS)

AF:

0.350

AC:

1686

AN:

4824

European-Finnish (FIN)

AF:

0.549

AC:

5799

AN:

10560

Middle Eastern (MID)

AF:

0.432

AC:

126

AN:

292

European-Non Finnish (NFE)

AF:

0.458

AC:

31160

AN:

67964

Other (OTH)

AF:

0.463

AC:

978

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1980

3959

5939

7918

9898

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

622

1244

1866

2488

3110

<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:

0.445

Hom.:

2643

Bravo

AF:

0.432

Asia WGS

AF:

0.417

AC:

1448

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.17

(source)

DANN

Benign

0.37

PhyloP100

-1.8

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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