X-152701444-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_005362.4(MAGEA3):c.612C>T(p.Ile204Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00471 in 1,208,506 control chromosomes in the GnomAD database, including 180 homozygotes. There are 1,529 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.024 ( 86 hom., 726 hem., cov: 21)
Exomes 𝑓: 0.0027 ( 94 hom. 803 hem. )
Consequence
MAGEA3
NM_005362.4 synonymous
NM_005362.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.14
Genes affected
MAGEA3 (HGNC:6801): (MAGE family member A3) 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. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant X-152701444-C-T is Benign according to our data. Variant chrX-152701444-C-T is described in ClinVar as [Benign]. Clinvar id is 780740.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.14 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0813 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAGEA3 | ENST00000370278.4 | c.612C>T | p.Ile204Ile | synonymous_variant | Exon 3 of 3 | 1 | NM_005362.4 | ENSP00000359301.3 | ||
MAGEA3 | ENST00000598245.2 | c.612C>T | p.Ile204Ile | synonymous_variant | Exon 3 of 3 | 2 | ENSP00000473093.1 | |||
MAGEA3 | ENST00000417212.5 | c.*17C>T | downstream_gene_variant | 2 | ENSP00000392758.1 |
Frequencies
GnomAD3 genomes AF: 0.0245 AC: 2735AN: 111764Hom.: 86 Cov.: 21 AF XY: 0.0214 AC XY: 726AN XY: 33980
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GnomAD4 exome AF: 0.00269 AC: 2950AN: 1096687Hom.: 94 Cov.: 31 AF XY: 0.00222 AC XY: 803AN XY: 362071
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GnomAD4 genome AF: 0.0245 AC: 2739AN: 111819Hom.: 86 Cov.: 21 AF XY: 0.0213 AC XY: 726AN XY: 34045
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
May 08, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at