rs918143
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032725.4(BUD13):c.1255-705G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,980 control chromosomes in the GnomAD database, including 12,961 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 0.41 ( 12961 hom., cov: 32)
Consequence
BUD13
NM_032725.4 intron
NM_032725.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.378
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 (NFE) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BUD13 | NM_032725.4 | c.1255-705G>A | intron_variant | ENST00000260210.5 | |||
BUD13 | NM_001159736.2 | c.853-705G>A | intron_variant | ||||
BUD13 | XM_011543035.3 | c.1156-705G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BUD13 | ENST00000260210.5 | c.1255-705G>A | intron_variant | 1 | NM_032725.4 | P2 | |||
BUD13 | ENST00000375445.7 | c.853-705G>A | intron_variant | 1 | A2 | ||||
BUD13 | ENST00000419189.1 | c.285-1944G>A | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.408 AC: 61919AN: 151862Hom.: 12967 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.407 AC: 61928AN: 151980Hom.: 12961 Cov.: 32 AF XY: 0.396 AC XY: 29431AN XY: 74286
GnomAD4 genome
?
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61928
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151980
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32
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29431
AN XY:
74286
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Asia WGS
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1014
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3478
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