rs4148727
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001134405.2(RUNDC3B):c.458+2795A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0485 in 152,192 control chromosomes in the GnomAD database, including 270 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (no stars).
Frequency
Genomes: 𝑓 0.048 ( 270 hom., cov: 32)
Exomes 𝑓: 0.063 ( 0 hom. )
Consequence
RUNDC3B
NM_001134405.2 intron
NM_001134405.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0550
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=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0898 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RUNDC3B | NM_001134405.2 | c.458+2795A>G | intron_variant | ENST00000394654.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RUNDC3B | ENST00000394654.4 | c.458+2795A>G | intron_variant | 2 | NM_001134405.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0485 AC: 7379AN: 152058Hom.: 270 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.0625 AC: 1AN: 16Hom.: 0 AF XY: 0.0833 AC XY: 1AN XY: 12
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GnomAD4 genome ? AF: 0.0485 AC: 7377AN: 152176Hom.: 270 Cov.: 32 AF XY: 0.0490 AC XY: 3643AN XY: 74402
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ClinVar
Significance: drug response
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Tramadol response Other:1
drug response, no assertion criteria provided | research | Bruce Budowle Laboratory, University of North Texas Health Science Center | Apr 28, 2018 | - T:M1 = postmortem ratio or tramadol to O-desmethyltramadol; t-MP = model-based clustered metabolizer phenotype inferred from T:M1 |
Computational scores
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Name
Calibrated prediction
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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