rs16913748
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_033278.4(TRIM3):c.603C>T(p.Ile201=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 1,613,888 control chromosomes in the GnomAD database, including 31,799 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 0.21 ( 3535 hom., cov: 33)
Exomes 𝑓: 0.19 ( 28264 hom. )
Consequence
TRIM3
NM_033278.4 synonymous
NM_033278.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.62
Genes affected
TRIM3 (HGNC:10064): (tripartite motif containing 3) The protein encoded by this gene is a member of the tripartite motif (TRIM) family, also called the 'RING-B-box-coiled-coil' (RBCC) subgroup of RING finger proteins. 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. This protein localizes to cytoplasmic filaments. It is similar to a rat protein which is a specific partner for the tail domain of myosin V, a class of myosins which are involved in the targeted transport of organelles. The rat protein can also interact with alpha-actinin-4. Thus it is suggested that this human protein may play a role in myosin V-mediated cargo transport. Alternatively spliced transcript variants encoding the same isoform have been identified. [provided by RefSeq, Jul 2008]
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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=-0.49).
BP7
?
Synonymous conserved (PhyloP=1.62 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM3 | NM_033278.4 | c.603C>T | p.Ile201= | synonymous_variant | 5/12 | ENST00000345851.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM3 | ENST00000345851.8 | c.603C>T | p.Ile201= | synonymous_variant | 5/12 | 1 | NM_033278.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.207 AC: 31434AN: 152124Hom.: 3531 Cov.: 33
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GnomAD3 exomes AF: 0.179 AC: 45047AN: 251218Hom.: 4617 AF XY: 0.183 AC XY: 24869AN XY: 135810
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GnomAD4 exome AF: 0.192 AC: 280205AN: 1461646Hom.: 28264 Cov.: 34 AF XY: 0.194 AC XY: 140798AN XY: 727124
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GnomAD4 genome ? AF: 0.207 AC: 31454AN: 152242Hom.: 3535 Cov.: 33 AF XY: 0.201 AC XY: 15000AN XY: 74454
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ClinVar
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