X-149716386-T-C
Position:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The ENST00000355220.6(MAGEA11):āc.900T>Cā(p.Asp300=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000826 in 1,210,137 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: š 0.0000089 ( 0 hom., 0 hem., cov: 23)
Exomes š: 0.0000082 ( 0 hom. 2 hem. )
Consequence
MAGEA11
ENST00000355220.6 synonymous
ENST00000355220.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.124
Genes affected
MAGEA11 (HGNC:6798): (MAGE family member A11) This gene is a member of the MAGEA gene family. The members of this family encode proteins with 50 to 80% sequence identity to each other. The promoters and first exons of the MAGEA genes show considerable variability, suggesting that the existence of this gene family enables the same function to be expressed under different transcriptional controls. The MAGEA genes are clustered at chromosomal location Xq28. They have been implicated in some hereditary disorders, such as dyskeratosis congenita. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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 (BayesDel_noAF=-0.93).
BP6
Variant X-149716386-T-C is Benign according to our data. Variant chrX-149716386-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3034896.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-0.124 with no splicing effect.
BS2
High Hemizygotes in GnomAdExome4 at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAGEA11 | NM_005366.5 | c.900T>C | p.Asp300= | synonymous_variant | 5/5 | ENST00000355220.6 | NP_005357.2 | |
MAGEA11 | NM_001011544.2 | c.813T>C | p.Asp271= | synonymous_variant | 5/5 | NP_001011544.1 | ||
MAGEA11 | XM_047442106.1 | c.900T>C | p.Asp300= | synonymous_variant | 8/8 | XP_047298062.1 | ||
MAGEA11 | XM_011531164.3 | c.876T>C | p.Asp292= | synonymous_variant | 4/4 | XP_011529466.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAGEA11 | ENST00000355220.6 | c.900T>C | p.Asp300= | synonymous_variant | 5/5 | 1 | NM_005366.5 | ENSP00000347358 | P2 | |
MAGEA11 | ENST00000333104.8 | c.813T>C | p.Asp271= | synonymous_variant | 4/4 | 5 | ENSP00000328177 | A2 | ||
MAGEA11 | ENST00000412632.6 | c.813T>C | p.Asp271= | synonymous_variant | 5/5 | 2 | ENSP00000391496 | |||
MAGEA11 | ENST00000518694.1 | n.2490T>C | non_coding_transcript_exon_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000893 AC: 1AN: 111934Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34100
GnomAD3 genomes
AF:
AC:
1
AN:
111934
Hom.:
Cov.:
23
AF XY:
AC XY:
0
AN XY:
34100
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183442Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67882
GnomAD3 exomes
AF:
AC:
1
AN:
183442
Hom.:
AF XY:
AC XY:
0
AN XY:
67882
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000820 AC: 9AN: 1098203Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 2AN XY: 363559
GnomAD4 exome
AF:
AC:
9
AN:
1098203
Hom.:
Cov.:
33
AF XY:
AC XY:
2
AN XY:
363559
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00000893 AC: 1AN: 111934Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34100
GnomAD4 genome
AF:
AC:
1
AN:
111934
Hom.:
Cov.:
23
AF XY:
AC XY:
0
AN XY:
34100
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
MAGEA11-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 12, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at