13-30459095-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002128.7(HMGB1):c.*2262G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,060 control chromosomes in the GnomAD database, including 3,754 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.20 ( 3754 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
HMGB1
NM_002128.7 3_prime_UTR
NM_002128.7 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.838
Genes affected
HMGB1 (HGNC:4983): (high mobility group box 1) This gene encodes a protein that belongs to the High Mobility Group-box superfamily. The encoded non-histone, nuclear DNA-binding protein regulates transcription, and is involved in organization of DNA. This protein plays a role in several cellular processes, including inflammation, cell differentiation and tumor cell migration. Multiple pseudogenes of this gene have been identified. Alternative splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 13-30459095-C-T is Benign according to our data. Variant chr13-30459095-C-T is described in ClinVar as [Benign]. Clinvar id is 1250264.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HMGB1 | NM_002128.7 | c.*2262G>A | 3_prime_UTR_variant | 5/5 | ENST00000341423.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HMGB1 | ENST00000341423.10 | c.*2262G>A | 3_prime_UTR_variant | 5/5 | 1 | NM_002128.7 | P1 | ||
HMGB1 | ENST00000405805.5 | c.*2262G>A | 3_prime_UTR_variant | 5/5 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.202 AC: 30699AN: 151942Hom.: 3749 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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GnomAD4 genome ? AF: 0.202 AC: 30703AN: 152060Hom.: 3754 Cov.: 32 AF XY: 0.202 AC XY: 14977AN XY: 74302
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 10, 2019 | This variant is associated with the following publications: (PMID: 28423715) - |
Computational scores
Source:
Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at