Variant 13-30461360-TTCA-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2

The NM_002128.7(HMGB1):c.642_644delTGA(p.Asp214del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000997 in 151,492 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0010 ( 0 hom., cov: 31)

Exomes 𝑓: 0.0013 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

HMGB1
NM_002128.7 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 6.72

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP6

Variant 13-30461360-TTCA-T is Benign according to our data. Variant chr13-30461360-TTCA-T is described in ClinVar as [Likely_benign]. Clinvar id is 2681315.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High AC in GnomAd4 at 151 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HMGB1	NM_002128.7 linkuse as main transcript	c.642_644delTGA	p.Asp214del	disruptive_inframe_deletion	5/5	ENST00000341423.10	NP_002119.1	P09429A0A024RDR0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HMGB1	ENST00000341423.10 linkuse as main transcript	c.642_644delTGA	p.Asp214del	disruptive_inframe_deletion	5/5	1	NM_002128.7	ENSP00000345347.5		P09429

Frequencies

GnomAD3 genomes

AF:

0.000998

AC:

151

AN:

151376

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000513

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00125

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.000832

Gnomad FIN

AF:

0.0000952

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00138

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000829

AC:

172

AN:

207392

Hom.:

AF XY:

0.000748

AC XY:

AN XY:

112370

show subpopulations

Gnomad AFR exome

AF:

0.000667

Gnomad AMR exome

AF:

0.00180

Gnomad ASJ exome

AF:

0.000951

Gnomad EAS exome

AF:

0.000865

Gnomad SAS exome

AF:

0.000655

Gnomad FIN exome

AF:

0.000104

Gnomad NFE exome

AF:

0.000768

Gnomad OTH exome

AF:

0.000628

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00125

AC:

1760

AN:

1404238

Hom.:

AF XY:

0.00127

AC XY:

884

AN XY:

694894

show subpopulations

Gnomad4 AFR exome

AF:

0.000553

Gnomad4 AMR exome

AF:

0.00184

Gnomad4 ASJ exome

AF:

0.00132

Gnomad4 EAS exome

AF:

0.000609

Gnomad4 SAS exome

AF:

0.000622

Gnomad4 FIN exome

AF:

0.0000589

Gnomad4 NFE exome

AF:

0.00140

Gnomad4 OTH exome

AF:

0.000899

GnomAD4 genome

AF:

0.000997

AC:

151

AN:

151492

Hom.:

Cov.:

AF XY:

0.000783

AC XY:

AN XY:

74074

show subpopulations

Gnomad4 AFR

AF:

0.000512

Gnomad4 AMR

AF:

0.00124

Gnomad4 ASJ

AF:

0.00144

Gnomad4 EAS

AF:

0.00135

Gnomad4 SAS

AF:

0.000833

Gnomad4 FIN

AF:

0.0000952

Gnomad4 NFE

AF:

0.00138

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000529

Hom.:

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

EBV-positive nodal T- and NK-cell lymphoma

Benign:1

Likely benign, no assertion criteria provided

research

Department of Clinical Pathology, School of Medicine, Fujita Health University

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over