1-54053434-G-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001305049.1(TMEM59):c.-283C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.052 in 530,254 control chromosomes in the GnomAD database, including 2,927 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 0.055 ( 738 hom., cov: 32)
Exomes 𝑓: 0.051 ( 2189 hom. )
Consequence
TMEM59
NM_001305049.1 5_prime_UTR
NM_001305049.1 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.82
Genes affected
TMEM59 (HGNC:1239): (transmembrane protein 59) This gene encodes a protein shown to regulate autophagy in response to bacterial infection. This protein may also regulate the retention of amyloid precursor protein (APP) in the Golgi apparatus through its control of APP glycosylation. Overexpression of this protein has been found to promote apoptosis in a glioma cell line. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]
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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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM59 | NM_001305049.1 | c.-283C>G | 5_prime_UTR_variant | Exon 1 of 8 | NP_001291978.1 | |||
TMEM59 | NM_001305051.1 | c.-283C>G | 5_prime_UTR_variant | Exon 1 of 8 | NP_001291980.1 | |||
TMEM59 | NM_001305052.1 | c.-177C>G | 5_prime_UTR_variant | Exon 1 of 7 | NP_001291981.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM59 | ENST00000371341.5 | c.-283C>G | 5_prime_UTR_variant | Exon 1 of 8 | 2 | ENSP00000360392.1 | ||||
TMEM59 | ENST00000440019.5 | c.-177C>G | 5_prime_UTR_variant | Exon 1 of 6 | 2 | ENSP00000399761.1 | ||||
TMEM59 | ENST00000452421.5 | c.-246C>G | upstream_gene_variant | 5 | ENSP00000397772.1 | |||||
TMEM59 | ENST00000420738.5 | c.-316C>G | upstream_gene_variant | 3 | ENSP00000413792.1 |
Frequencies
GnomAD3 genomes AF: 0.0544 AC: 8271AN: 152140Hom.: 727 Cov.: 32
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GnomAD4 exome AF: 0.0509 AC: 19255AN: 377996Hom.: 2189 Cov.: 4 AF XY: 0.0489 AC XY: 9618AN XY: 196818
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GnomAD4 genome AF: 0.0545 AC: 8301AN: 152258Hom.: 738 Cov.: 32 AF XY: 0.0589 AC XY: 4382AN XY: 74454
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at