rs438259
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000645747.1(HULC):n.508-16317G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,040 control chromosomes in the GnomAD database, including 5,820 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 0.27 ( 5820 hom., cov: 32)
Consequence
HULC
ENST00000645747.1 intron, non_coding_transcript
ENST00000645747.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.15
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]
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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=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC105374914 | XR_001743953.1 | n.279-16317G>A | intron_variant, non_coding_transcript_variant | ||||
LOC105374914 | XR_001743951.1 | n.585-16317G>A | intron_variant, non_coding_transcript_variant | ||||
LOC105374914 | XR_001743952.1 | n.279-16317G>A | intron_variant, non_coding_transcript_variant | ||||
LOC105374914 | XR_926450.3 | n.401-16317G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HULC | ENST00000645747.1 | n.508-16317G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.274 AC: 41663AN: 151922Hom.: 5812 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.274 AC: 41696AN: 152040Hom.: 5820 Cov.: 32 AF XY: 0.273 AC XY: 20282AN XY: 74286
GnomAD4 genome
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32
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20282
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74286
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915
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at