rs2239775
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002872.5(RAC2):c.36-143G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 739,974 control chromosomes in the GnomAD database, including 9,234 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 0.17 ( 2534 hom., cov: 33)
Exomes 𝑓: 0.14 ( 6700 hom. )
Consequence
RAC2
NM_002872.5 intron
NM_002872.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.79
Genes affected
RAC2 (HGNC:9802): (Rac family small GTPase 2) This gene encodes a member of the Ras superfamily of small guanosine triphosphate (GTP)-metabolizing proteins. The encoded protein localizes to the plasma membrane, where it regulates diverse processes, such as secretion, phagocytosis, and cell polarization. Activity of this protein is also involved in the generation of reactive oxygen species. Mutations in this gene are associated with neutrophil immunodeficiency syndrome. There is a pseudogene for this gene on chromosome 6. [provided by RefSeq, Jul 2013]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAC2 | NM_002872.5 | c.36-143G>T | intron_variant | ENST00000249071.11 | |||
RAC2 | XM_006724286.4 | c.36-143G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAC2 | ENST00000249071.11 | c.36-143G>T | intron_variant | 1 | NM_002872.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.173 AC: 26368AN: 152070Hom.: 2524 Cov.: 33
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GnomAD4 exome AF: 0.145 AC: 85099AN: 587786Hom.: 6700 AF XY: 0.144 AC XY: 45744AN XY: 316784
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GnomAD4 genome ? AF: 0.174 AC: 26415AN: 152188Hom.: 2534 Cov.: 33 AF XY: 0.170 AC XY: 12669AN XY: 74414
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ClinVar
Not reported inComputational scores
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Name
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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