X-30218661-TC-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_002364.5(MAGEB2):​c.83delC​(p.Pro28LeufsTer84) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: not found (cov: 24)

Consequence

MAGEB2
NM_002364.5 frameshift

Scores

Not classified

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 0.403
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAGEB2NM_002364.5 linkc.83delC p.Pro28LeufsTer84 frameshift_variant Exon 2 of 2 ENST00000378988.5 NP_002355.2 O15479Q53G50
MAGEB2XM_011545512.2 linkc.83delC p.Pro28LeufsTer84 frameshift_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.83delC p.Pro28LeufsTer84 frameshift_variant Exon 2 of 2 1 NM_002364.5 ENSP00000368273.4 O15479

Frequencies

GnomAD3 genomes
Cov.:
24
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
24

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Autism Uncertain:1
-
Centre for Addiction & Mental Health, Centre for Addiction & Mental Health
Significance: Uncertain significance
Review Status: no assertion criteria provided
Collection Method: research

Gene not previously associated with disease; independent supportng evidence needed -

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

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-30236778; API