rs560820937
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_001080495.3(TNRC18):c.8700+3A>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000019 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000054 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TNRC18
NM_001080495.3 splice_region, intron
NM_001080495.3 splice_region, intron
Scores
2
Splicing: ADA: 0.9962
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.572
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNRC18 | ENST00000430969.6 | c.8700+3A>T | splice_region_variant, intron_variant | Intron 29 of 29 | 5 | NM_001080495.3 | ENSP00000395538.1 | |||
TNRC18 | ENST00000399537.8 | c.8700+3A>T | splice_region_variant, intron_variant | Intron 29 of 29 | 5 | ENSP00000382452.4 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1AN: 51752Hom.: 0 Cov.: 0 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000540 AC: 23AN: 425974Hom.: 0 Cov.: 28 AF XY: 0.0000589 AC XY: 13AN XY: 220816
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000193 AC: 1AN: 51776Hom.: 0 Cov.: 0 AF XY: 0.0000404 AC XY: 1AN XY: 24772
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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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dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at