Genetic Variant MAGEB3:p.Thr8Met (chrX-30235947-C-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_002365.5(MAGEB3):c.23C>T(p.Thr8Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00012 in 1,204,830 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 45 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T8A) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.00013 ( 0 hom., 6 hem., cov: 22)

Exomes 𝑓: 0.00012 ( 0 hom. 39 hem. )

Consequence

MAGEB3
NM_002365.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.105

Variant links:

Genes affected

MAGEB3 (HGNC:6810): (MAGE family member B3) This gene is a MAGE-B subfamily member of the MAGE gene family. MAGE family member proteins direct the expression of tumor antigens recognized on a human melanoma by autologous cytolytic T lymphocytes. There are two known clusters of MAGE genes on chromosome X. The members of the MAGE-A subfamily are located in the Xq28 region, while the members of the MAGE-B subfamily are clustered in the Xp21 region. [provided by RefSeq, Jul 2008]

MAGEB3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.03599748).

BS2

High Hemizygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAGEB3	NM_002365.5 link	c.23C>T	p.Thr8Met	missense_variant	Exon 5 of 5	ENST00000361644.4	NP_002356.2	O15480
MAGEB3	NM_001386865.1 link	c.23C>T	p.Thr8Met	missense_variant	Exon 3 of 3		NP_001373794.1
MAGEB3	XM_011545513.3 link	c.23C>T	p.Thr8Met	missense_variant	Exon 4 of 4		XP_011543815.1	O15480

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAGEB3	ENST00000361644.4 link	c.23C>T	p.Thr8Met	missense_variant	Exon 5 of 5	2	NM_002365.5	ENSP00000355198.2		O15480
MAGEB3	ENST00000620842.1 link	c.23C>T	p.Thr8Met	missense_variant	Exon 1 of 1	6		ENSP00000478513.1		O15480

Frequencies

GnomAD3 genomes

AF:

0.000126

AC:

AN:

111350

Hom.:

Cov.:

AF XY:

0.000179

AC XY:

AN XY:

33536

show subpopulations

Gnomad AFR

AF:

0.0000327

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000755

Gnomad OTH

AF:

0.000674

GnomAD3 exomes

AF:

0.000120

AC:

AN:

175066

Hom.:

AF XY:

0.0000995

AC XY:

AN XY:

60276

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000607

Gnomad FIN exome

AF:

0.000578

Gnomad NFE exome

AF:

0.000102

Gnomad OTH exome

AF:

0.000699

GnomAD4 exome

AF:

0.000120

AC:

131

AN:

1093480

Hom.:

Cov.:

AF XY:

0.000108

AC XY:

AN XY:

359622

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000189

Gnomad4 FIN exome

AF:

0.000892

Gnomad4 NFE exome

AF:

0.0000976

Gnomad4 OTH exome

AF:

0.000240

GnomAD4 genome

AF:

0.000126

AC:

AN:

111350

Hom.:

Cov.:

AF XY:

0.000179

AC XY:

AN XY:

33536

show subpopulations

Gnomad4 AFR

AF:

0.0000327

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00132

Gnomad4 NFE

AF:

0.0000755

Gnomad4 OTH

AF:

0.000674

Alfa

AF:

0.000103

Hom.:

Bravo

AF:

0.0000340

TwinsUK

AF:

0.000539

AC:

ALSPAC

AF:

0.00

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000149

AC:

ExAC

AF:

0.000132

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

May 21, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.23C>T (p.T8M) alteration is located in exon 5 (coding exon 1) of the MAGEB3 gene. This alteration results from a C to T substitution at nucleotide position 23, causing the threonine (T) at amino acid position 8 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.097

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.4

DANN

Uncertain

0.98

DEOGEN2

Benign

0.0037

T;T

FATHMM_MKL

Benign

0.013

LIST_S2

Uncertain

0.89

.;D

M_CAP

Benign

0.0040

MetaRNN

Benign

0.036

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.1

L;L

PrimateAI

Benign

0.33

PROVEAN

Benign

-0.10

N;.

REVEL

Benign

0.075

Sift

Uncertain

0.0010

D;.

Sift4G

Pathogenic

0.0010

D;D

Polyphen

0.97

D;D

Vest4

0.11

MVP

0.043

MPC

0.13

ClinPred

0.32

GERP RS

-1.8

Varity_R

0.058

gMVP

0.17

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