17-58998293-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP4_StrongBS2
The NM_015294.6(TRIM37):c.*1084C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000507 in 985,268 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00012 ( 1 hom., cov: 33)
Exomes 𝑓: 0.000037 ( 0 hom. )
Consequence
TRIM37
NM_015294.6 3_prime_UTR
NM_015294.6 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.478
Genes affected
TRIM37 (HGNC:7523): (tripartite motif containing 37) This gene encodes a member of the tripartite motif (TRIM) family, whose members are involved in diverse cellular functions such as developmental patterning and oncogenesis. The TRIM motif includes zinc-binding domains, a RING finger region, a B-box motif and a coiled-coil domain. The RING finger and B-box domains chelate zinc and might be involved in protein-protein and/or protein-nucleic acid interactions. Mutations in this gene are associated with mulibrey (muscle-liver-brain-eye) nanism, an autosomal recessive disorder that involves several tissues of mesodermal origin. TRIM37 localizes in peroxisomal membranes, and has been implicated in human peroxisomal biogenesis disorders. [provided by RefSeq, Jul 2020]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BS2
?
High Homozygotes in GnomAd at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM37 | NM_015294.6 | c.*1084C>T | 3_prime_UTR_variant | 24/24 | ENST00000262294.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM37 | ENST00000262294.12 | c.*1084C>T | 3_prime_UTR_variant | 24/24 | 1 | NM_015294.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152150Hom.: 2 Cov.: 33
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GnomAD4 exome AF: 0.0000372 AC: 31AN: 833000Hom.: 0 Cov.: 28 AF XY: 0.0000442 AC XY: 17AN XY: 384662
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GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152268Hom.: 1 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74454
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Mulibrey nanism syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | - - |
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