13-30459175-C-CTTAA
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_002128.7(HMGB1):c.*2181_*2182insTTAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.28 ( 5979 hom., cov: 19)
Failed GnomAD Quality Control
Consequence
HMGB1
NM_002128.7 3_prime_UTR
NM_002128.7 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.255
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 -10 ACMG points.
BP6
Variant 13-30459175-C-CTTAA is Benign according to our data. Variant chr13-30459175-C-CTTAA is described in ClinVar as [Benign]. Clinvar id is 1289616.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HMGB1 | NM_002128.7 | c.*2181_*2182insTTAA | 3_prime_UTR_variant | 5/5 | ENST00000341423.10 | NP_002119.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.276 AC: 41817AN: 151698Hom.: 5972 Cov.: 19
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
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GnomAD4 genome AF: 0.276 AC: 41846AN: 151814Hom.: 5979 Cov.: 19 AF XY: 0.272 AC XY: 20206AN XY: 74172
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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 | Apr 28, 2020 | This variant is associated with the following publications: (PMID: 31777261) - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at