Variant 13-30461402-TTCC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_002128.7(HMGB1):c.600_602delGGA(p.Glu201del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000421 in 151,882 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00042 ( 0 hom., cov: 31)

Exomes 𝑓: 0.00040 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

HMGB1
NM_002128.7 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 7.02

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 -6 ACMG points.

BP6

Variant 13-30461402-TTCC-T is Benign according to our data. Variant chr13-30461402-TTCC-T is described in ClinVar as [Benign]. Clinvar id is 2643710.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 64 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HMGB1	NM_002128.7 linkuse as main transcript	c.600_602delGGA	p.Glu201del	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.600_602delGGA	p.Glu201del	disruptive_inframe_deletion	5/5	1	NM_002128.7	ENSP00000345347.5		P09429

Frequencies

GnomAD3 genomes

AF:

0.000422

AC:

AN:

151764

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000704

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000262

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.000379

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000250

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000493

AC:

AN:

131744

Hom.:

AF XY:

0.000600

AC XY:

AN XY:

70052

show subpopulations

Gnomad AFR exome

AF:

0.000128

Gnomad AMR exome

AF:

0.000935

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000378

Gnomad SAS exome

AF:

0.00193

Gnomad FIN exome

AF:

0.000211

Gnomad NFE exome

AF:

0.000128

Gnomad OTH exome

AF:

0.000278

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000398

AC:

568

AN:

1426462

Hom.:

AF XY:

0.000412

AC XY:

292

AN XY:

708148

show subpopulations

Gnomad4 AFR exome

AF:

0.000415

Gnomad4 AMR exome

AF:

0.000859

Gnomad4 ASJ exome

AF:

0.0000412

Gnomad4 EAS exome

AF:

0.00162

Gnomad4 SAS exome

AF:

0.00171

Gnomad4 FIN exome

AF:

0.000154

Gnomad4 NFE exome

AF:

0.000262

Gnomad4 OTH exome

AF:

0.000392

GnomAD4 genome

AF:

0.000421

AC:

AN:

151882

Hom.:

Cov.:

AF XY:

0.000391

AC XY:

AN XY:

74244

show subpopulations

Gnomad4 AFR

AF:

0.000702

Gnomad4 AMR

AF:

0.000262

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.00124

Gnomad4 FIN

AF:

0.000379

Gnomad4 NFE

AF:

0.000250

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.000325

Asia WGS

AF:

0.000289

AC:

AN:

3476

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

CeGaT Center for Human Genetics Tuebingen

May 01, 2023

HMGB1: BS1, BS2 -

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