X-30218648-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_002364.5(MAGEB2):​c.68G>A​(p.Arg23Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 23)
Exomes 𝑓: 0.0000027 ( 0 hom. 2 hem. )
Failed GnomAD Quality Control

Consequence

MAGEB2
NM_002364.5 missense

Scores

17

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0740
Variant links:
Genes affected
MAGEB2 (HGNC:6809): (MAGE family member B2) This gene is a member of the MAGEB gene family. The members of this family have their entire coding sequences located in the last exon, and the encoded proteins show 50 to 68% sequence identity to each other. The promoters and first exons of the MAGEB genes show considerable variability, suggesting that the existence of this gene family enables the same function to be expressed under different transcriptional controls. This gene is localized in the DSS (dosage-sensitive sex reversal) critical region. It is expressed in testis and placenta, and in a significant fraction of tumors of various histological types. The MAGEB genes are clustered on chromosome Xp22-p21. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.02463308).
BP6
Variant X-30218648-G-A is Benign according to our data. Variant chrX-30218648-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3542052.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAGEB2NM_002364.5 linkc.68G>A p.Arg23Gln missense_variant Exon 2 of 2 ENST00000378988.5 NP_002355.2 O15479Q53G50
MAGEB2XM_011545512.2 linkc.68G>A p.Arg23Gln missense_variant Exon 2 of 2 XP_011543814.1 O15479

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAGEB2ENST00000378988.5 linkc.68G>A p.Arg23Gln missense_variant Exon 2 of 2 1 NM_002364.5 ENSP00000368273.4 O15479

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD3 exomes
AF:
0.00000557
AC:
1
AN:
179512
Hom.:
0
AF XY:
0.0000156
AC XY:
1
AN XY:
64184
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:
0.0000544
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00000274
AC:
3
AN:
1096345
Hom.:
0
Cov.:
32
AF XY:
0.00000553
AC XY:
2
AN XY:
361755
show subpopulations
Gnomad4 AFR exome
AF:
0.0000379
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000186
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000217
GnomAD4 genome
Cov.:
23

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
Aug 28, 2024
Ambry Genetics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.072
BayesDel_addAF
Benign
-0.61
T
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.28
DANN
Benign
0.34
DEOGEN2
Benign
0.0019
T
FATHMM_MKL
Benign
0.0035
N
LIST_S2
Benign
0.18
T
M_CAP
Benign
0.0018
T
MetaRNN
Benign
0.025
T
MetaSVM
Benign
-0.94
T
MutationAssessor
Benign
-1.9
N
PrimateAI
Benign
0.31
T
PROVEAN
Benign
2.5
N
REVEL
Benign
0.029
Sift
Benign
1.0
T
Sift4G
Benign
1.0
T
Polyphen
0.0
B
Vest4
0.045
MutPred
0.38
Loss of methylation at R23 (P = 0.012);
MVP
0.18
MPC
0.0024
ClinPred
0.024
T
GERP RS
0.96
Varity_R
0.031
gMVP
0.068

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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.

Other links and lift over

dbSNP: rs1396356517; hg19: chrX-30236765; COSMIC: COSV66781776; API