13-30461330-GAAA-GAA

Position:

• chr13-30461330-GAAA-GAA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_002128.7(HMGB1):​c.*26del variant causes a 3 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 0.067 (1057 hom., cov: 17)
  • Exomes 𝑓: 0.0049 (339 hom.)
  • Failed GnomAD Quality Control
• Consequence: HMGB1 NM_002128.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HMGB1	NM_002128.7	c.*26del		3_prime_UTR_variant	5/5	ENST00000341423.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HMGB1	ENST00000341423.10	c.*26del		3_prime_UTR_variant	5/5	1	NM_002128.7	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 9665 AN: 145332 Hom.: 1054 Cov.: 17 FAILED QC

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0273

Gnomad ASJ AF: 0.00700

Gnomad EAS AF: 0.00234

Gnomad SAS AF: 0.00169

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00112

Gnomad OTH AF: 0.0427

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00488 AC: 6436 AN: 1318820 Hom.: 339 Cov.: 32 AF XY: 0.00430 AC XY: 2794 AN XY: 649738

Gnomad4 AFR exome AF: 0.173

Gnomad4 AMR exome AF: 0.0128

Gnomad4 ASJ exome AF: 0.00441

Gnomad4 EAS exome AF: 0.00611

Gnomad4 SAS exome AF: 0.000866

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000528

Gnomad4 OTH exome AF: 0.0130

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0666 AC: 9687 AN: 145418 Hom.: 1057 Cov.: 17 AF XY: 0.0637 AC XY: 4511 AN XY: 70802

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.0273

Gnomad4 ASJ AF: 0.00700

Gnomad4 EAS AF: 0.00235

Gnomad4 SAS AF: 0.00149

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00112

Gnomad4 OTH AF: 0.0424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs41376448; hg19: chr13-31035467;