Variant rs1328866 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000503668.2(HULC):n.255-262T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,944 control chromosomes in the GnomAD database, including 18,070 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 0.48 ( 18070 hom., cov: 31)

Failed GnomAD Quality Control

Consequence

HULC
ENST00000503668.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.127

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
HULC	NR_004855.3 link	n.123-262T>A	intron_variant
LOC100506207	NR_038979.1 link	n.685-57326T>A	intron_variant
LOC100506207	NR_038980.1 link	n.707+94640T>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
HULC	ENST00000503668.2 link	n.255-262T>A	intron_variant	1
HULC	ENST00000642163.1 link	n.700+94640T>A	intron_variant
HULC	ENST00000642168.1 link	n.798-262T>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.483

AC:

73390

AN:

151826

Hom.:

18064

Cov.:

show subpopulations

Gnomad AFR

AF:

0.526

Gnomad AMI

AF:

0.359

Gnomad AMR

AF:

0.460

Gnomad ASJ

AF:

0.414

Gnomad EAS

AF:

0.481

Gnomad SAS

AF:

0.372

Gnomad FIN

AF:

0.578

Gnomad MID

AF:

0.434

Gnomad NFE

AF:

0.461

Gnomad OTH

AF:

0.499

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

GnomAD4 genome

AF:

0.483

AC:

73442

AN:

151944

Hom.:

18070

Cov.:

AF XY:

0.487

AC XY:

36179

AN XY:

74234

show subpopulations

Gnomad4 AFR

AF:

0.526

Gnomad4 AMR

AF:

0.460

Gnomad4 ASJ

AF:

0.414

Gnomad4 EAS

AF:

0.481

Gnomad4 SAS

AF:

0.371

Gnomad4 FIN

AF:

0.578

Gnomad4 NFE

AF:

0.461

Gnomad4 OTH

AF:

0.501

Alfa

AF:

0.481

Hom.:

2193

Bravo

AF:

0.480

Asia WGS

AF:

0.459

AC:

1596

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

8.3

DANN

Benign

0.61

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