rs3744028
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173547.4(TRIM65):c.511-91A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 1,322,824 control chromosomes in the GnomAD database, including 29,428 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 0.26 ( 6678 hom., cov: 33)
Exomes 𝑓: 0.19 ( 22750 hom. )
Consequence
TRIM65
NM_173547.4 intron
NM_173547.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.698
Genes affected
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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=-0.86).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM65 | NM_173547.4 | c.511-91A>G | intron_variant | ENST00000269383.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM65 | ENST00000269383.8 | c.511-91A>G | intron_variant | 1 | NM_173547.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.263 AC: 39914AN: 151996Hom.: 6652 Cov.: 33
GnomAD3 genomes
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GnomAD4 exome AF: 0.188 AC: 219614AN: 1170710Hom.: 22750 Cov.: 16 AF XY: 0.188 AC XY: 109532AN XY: 583020
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GnomAD4 genome ? AF: 0.263 AC: 39995AN: 152114Hom.: 6678 Cov.: 33 AF XY: 0.257 AC XY: 19129AN XY: 74346
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at