rs2074474
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001369521.2(TRIM39):āc.939T>Cā(p.Pro313Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 1,611,674 control chromosomes in the GnomAD database, including 56,734 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: š 0.28 ( 6480 hom., cov: 31)
Exomes š: 0.25 ( 50254 hom. )
Consequence
TRIM39
NM_001369521.2 synonymous
NM_001369521.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.61
Genes affected
TRIM39 (HGNC:10065): (tripartite motif containing 39) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The function of this protein has not been identified. This gene lies within the major histocompatibility complex class I region on chromosome 6. Alternate splicing results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
TRIM39-RPP21 (HGNC:38845): (TRIM39-RPP21 readthrough) This locus represents naturally occurring read-through transcription between the neighboring TRIM39 (tripartite motif-containing 39) and RPP21 (ribonuclease P/MRP 21kDa subunit) genes on chromosome 6. The read-through transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP7
Synonymous conserved (PhyloP=-3.61 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIM39 | NM_001369521.2 | c.939T>C | p.Pro313Pro | synonymous_variant | 8/8 | ENST00000396551.9 | NP_001356450.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIM39 | ENST00000396551.9 | c.939T>C | p.Pro313Pro | synonymous_variant | 8/8 | 5 | NM_001369521.2 | ENSP00000379800.3 | ||
TRIM39-RPP21 | ENST00000623385.3 | c.939T>C | p.Pro313Pro | synonymous_variant | 7/11 | 5 | ENSP00000485378.1 |
Frequencies
GnomAD3 genomes AF: 0.282 AC: 42870AN: 151908Hom.: 6470 Cov.: 31
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GnomAD3 exomes AF: 0.306 AC: 74939AN: 244764Hom.: 12773 AF XY: 0.300 AC XY: 40062AN XY: 133466
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GnomAD4 exome AF: 0.250 AC: 364213AN: 1459648Hom.: 50254 Cov.: 34 AF XY: 0.251 AC XY: 182511AN XY: 726084
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GnomAD4 genome AF: 0.282 AC: 42923AN: 152026Hom.: 6480 Cov.: 31 AF XY: 0.287 AC XY: 21329AN XY: 74300
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Not reported inComputational scores
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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