13-30464144-TA-T

Position:

• chr13-30464144-TA-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000399489.5(HMGB1):​c.-465delT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.95 (67581 hom., cov: 0)
  • Exomes 𝑓: 0.78 (175298 hom.)
• Consequence: HMGB1 ENST00000399489.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403

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]

HMGB1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HMGB1	NM_002128.7	c.-14-451delT		intron_variant		ENST00000341423.10	NP_002119.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HMGB1	ENST00000341423.10	c.-14-451delT		intron_variant		1	NM_002128.7	ENSP00000345347.5

Frequencies

GnomAD3 genomes AF: 0.949 AC: 141992 AN: 149568 Hom.: 67561 Cov.: 0

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.969

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.986

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.976

Gnomad OTH AF: 0.963

GnomAD4 exome AF: 0.778 AC: 490046 AN: 630022 Hom.: 175298 Cov.: 0 AF XY: 0.779 AC XY: 227370 AN XY: 292006

Gnomad4 AFR exome AF: 0.740

Gnomad4 AMR exome AF: 0.787

Gnomad4 ASJ exome AF: 0.784

Gnomad4 EAS exome AF: 0.792

Gnomad4 SAS exome AF: 0.770

Gnomad4 FIN exome AF: 0.802

Gnomad4 NFE exome AF: 0.779

Gnomad4 OTH exome AF: 0.778

GnomAD4 genome AF: 0.949 AC: 142057 AN: 149666 Hom.: 67581 Cov.: 0 AF XY: 0.950 AC XY: 69375 AN XY: 72994

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.969

Gnomad4 ASJ AF: 0.967

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.971

Gnomad4 FIN AF: 0.986

Gnomad4 NFE AF: 0.976

Gnomad4 OTH AF: 0.963

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs5802568; hg19: chr13-31038281;