rs690232
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017594.5(DIRAS2):c.-36-6293C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,010 control chromosomes in the GnomAD database, including 6,560 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 0.29 ( 6560 hom., cov: 32)
Consequence
DIRAS2
NM_017594.5 intron
NM_017594.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.639
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=-0.96).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIRAS2 | NM_017594.5 | c.-36-6293C>T | intron_variant | ENST00000375765.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DIRAS2 | ENST00000375765.5 | c.-36-6293C>T | intron_variant | 1 | NM_017594.5 | P1 | |||
DIRAS2 | ENST00000636786.1 | c.-37+5902C>T | intron_variant | 4 | |||||
DIRAS2 | ENST00000637905.1 | c.-37+5720C>T | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.293 AC: 44476AN: 151890Hom.: 6547 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: 0.293 AC: 44526AN: 152010Hom.: 6560 Cov.: 32 AF XY: 0.294 AC XY: 21869AN XY: 74288
GnomAD4 genome
?
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44526
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152010
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32
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21869
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74288
Gnomad4 AFR
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Asia WGS
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1333
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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