Variant 5-150012282-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_014983.3(HMGXB3):c.838C>T(p.Pro280Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00927 in 1,552,110 control chromosomes in the GnomAD database, including 98 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0069 ( 6 hom., cov: 32)

Exomes 𝑓: 0.0095 ( 92 hom. )

Consequence

HMGXB3
NM_014983.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.79

Variant links:

Genes affected

HMGXB3 (HGNC:28982): (HMG-box containing 3) This gene is one of the non-canonical high mobility group (HMG) genes. The encoded protein contains an HMG-box domain found in DNA binding proteins such as transcription factors and chromosomal proteins. [provided by RefSeq, Aug 2011]

HMGXB3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0049375296).

BP6

Variant 5-150012282-C-T is Benign according to our data. Variant chr5-150012282-C-T is described in ClinVar as [Benign]. Clinvar id is 773464.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
HMGXB3	NM_014983.3 linkuse as main transcript	c.838C>T	p.Pro280Ser	missense_variant	5/20	ENST00000502717.6
HMGXB3	NM_001366501.2 linkuse as main transcript	c.340C>T	p.Pro114Ser	missense_variant	4/19
HMGXB3	XM_047416963.1 linkuse as main transcript	c.838C>T	p.Pro280Ser	missense_variant	5/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
HMGXB3	ENST00000502717.6 linkuse as main transcript	c.838C>T	p.Pro280Ser	missense_variant	5/20	1	NM_014983.3	P2
HMGXB3	ENST00000613459.4 linkuse as main transcript	c.1576C>T	p.Pro526Ser	missense_variant	6/21	5		A2
HMGXB3	ENST00000503427.5 linkuse as main transcript	c.838C>T	p.Pro280Ser	missense_variant	5/21	5		A2

Frequencies

GnomAD3 genomes

AF:

0.00690

AC:

1050

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00234

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0100

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000828

Gnomad FIN

AF:

0.00235

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0110

Gnomad OTH

AF:

0.00862

GnomAD3 exomes

AF:

0.00588

AC:

935

AN:

158950

Hom.:

AF XY:

0.00552

AC XY:

462

AN XY:

83706

show subpopulations

Gnomad AFR exome

AF:

0.00168

Gnomad AMR exome

AF:

0.00670

Gnomad ASJ exome

AF:

0.00141

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000527

Gnomad FIN exome

AF:

0.00257

Gnomad NFE exome

AF:

0.0106

Gnomad OTH exome

AF:

0.00706

GnomAD4 exome

AF:

0.00953

AC:

13344

AN:

1399814

Hom.:

Cov.:

AF XY:

0.00915

AC XY:

6315

AN XY:

690414

show subpopulations

Gnomad4 AFR exome

AF:

0.00152

Gnomad4 AMR exome

AF:

0.00644

Gnomad4 ASJ exome

AF:

0.00127

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000707

Gnomad4 FIN exome

AF:

0.00282

Gnomad4 NFE exome

AF:

0.0114

Gnomad4 OTH exome

AF:

0.00844

GnomAD4 genome

AF:

0.00689

AC:

1050

AN:

152296

Hom.:

Cov.:

AF XY:

0.00681

AC XY:

507

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.00233

Gnomad4 AMR

AF:

0.0101

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000829

Gnomad4 FIN

AF:

0.00235

Gnomad4 NFE

AF:

0.0110

Gnomad4 OTH

AF:

0.00853

Alfa

AF:

0.00912

Hom.:

Bravo

AF:

0.00672

TwinsUK

AF:

0.0129

AC:

ALSPAC

AF:

0.0135

AC:

ESP6500AA

AF:

0.00145

AC:

ESP6500EA

AF:

0.00974

AC:

ExAC

AF:

0.00338

AC:

Asia WGS

AF:

0.000577

AC:

AN:

3478

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

Invitae

Dec 27, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.18

BayesDel_noAF

Uncertain

-0.020

Cadd

Benign

Dann

Uncertain

0.99

DEOGEN2

Benign

0.020

T;T;.

Eigen

Uncertain

0.22

Eigen_PC

Uncertain

0.39

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Benign

0.83

T;T;T

M_CAP

Benign

0.010

MetaRNN

Benign

0.0049

T;T;T

MetaSVM

Benign

-0.68

MutationAssessor

Benign

0.97

L;.;.

MutationTaster

Benign

1.0

D;D

PrimateAI

Benign

0.43

Sift4G

Benign

0.068

T;D;D

Polyphen

0.18

B;.;.

Vest4

0.26

MVP

0.12

ClinPred

0.023

GERP RS

6.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.40

gMVP

0.32

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