rs930421
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001330442.2(MTA3):c.*700A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 985,122 control chromosomes in the GnomAD database, including 55,368 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.35 ( 9325 hom., cov: 32)
Exomes 𝑓: 0.33 ( 46043 hom. )
Consequence
MTA3
NM_001330442.2 3_prime_UTR
NM_001330442.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.336
Genes affected
MTA3 (HGNC:23784): (metastasis associated 1 family member 3) Predicted to enable histone deacetylase binding activity; transcription coactivator activity; and transcription corepressor activity. Involved in negative regulation of transcription, DNA-templated. Located in nucleoplasm. Part of NuRD complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTA3 | NM_001330442.2 | c.*700A>G | 3_prime_UTR_variant | 17/17 | ENST00000405094.2 | NP_001317371.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTA3 | ENST00000405094.2 | c.*700A>G | 3_prime_UTR_variant | 17/17 | 5 | NM_001330442.2 | ENSP00000385823 | A1 | ||
MTA3 | ENST00000406652.5 | c.*700A>G | 3_prime_UTR_variant | 17/17 | 1 | ENSP00000384249 | ||||
MTA3 | ENST00000405592.5 | c.*700A>G | 3_prime_UTR_variant | 18/18 | 2 | ENSP00000383973 | ||||
MTA3 | ENST00000409019.5 | downstream_gene_variant | 5 | ENSP00000386763 |
Frequencies
GnomAD3 genomes AF: 0.346 AC: 52589AN: 151864Hom.: 9328 Cov.: 32
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GnomAD4 exome AF: 0.332 AC: 276398AN: 833136Hom.: 46043 Cov.: 29 AF XY: 0.332 AC XY: 127761AN XY: 384738
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GnomAD4 genome AF: 0.346 AC: 52616AN: 151986Hom.: 9325 Cov.: 32 AF XY: 0.344 AC XY: 25560AN XY: 74258
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at