Variant rs2876143 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000642760.1(HULC):n.924-8774A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,990 control chromosomes in the GnomAD database, including 6,654 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 0.26 ( 6654 hom., cov: 32)

Consequence

HULC
ENST00000642760.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.871

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:

LOC105374914 (HGNC:):

LOC105374914 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC105374914	XR_001743951.1 link	n.455-8774A>G	intron_variant
LOC105374914	XR_001743952.1 link	n.149-8774A>G	intron_variant
LOC105374914	XR_001743953.1 link	n.149-8774A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect
HULC	ENST00000642760.1 link	n.924-8774A>G	intron_variant
HULC	ENST00000642798.1 link	n.691-8774A>G	intron_variant
HULC	ENST00000643431.1 link	n.1149-2339A>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.265

AC:

40203

AN:

151872

Hom.:

6644

Cov.:

show subpopulations

Gnomad AFR

AF:

0.470

Gnomad AMI

AF:

0.214

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.202

Gnomad EAS

AF:

0.185

Gnomad SAS

AF:

0.115

Gnomad FIN

AF:

0.144

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.192

Gnomad OTH

AF:

0.248

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.265

AC:

40245

AN:

151990

Hom.:

6654

Cov.:

AF XY:

0.260

AC XY:

19327

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.470

Gnomad4 AMR

AF:

0.211

Gnomad4 ASJ

AF:

0.202

Gnomad4 EAS

AF:

0.186

Gnomad4 SAS

AF:

0.115

Gnomad4 FIN

AF:

0.144

Gnomad4 NFE

AF:

0.192

Gnomad4 OTH

AF:

0.245

Alfa

AF:

0.258

Hom.:

1146

Bravo

AF:

0.284

Asia WGS

AF:

0.186

AC:

648

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.44

DANN

Benign

0.44

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over