rs3729790
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006908.5(RAC1):c.107+40G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 1,340,934 control chromosomes in the GnomAD database, including 31,978 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 ( 2516 hom., cov: 32)
Exomes 𝑓: 0.22 ( 29462 hom. )
Consequence
RAC1
NM_006908.5 intron
NM_006908.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -5.33
Genes affected
RAC1 (HGNC:9801): (Rac family small GTPase 1) The protein encoded by this gene is a GTPase which belongs to the RAS superfamily of small GTP-binding proteins. Members of this superfamily appear to regulate a diverse array of cellular events, including the control of cell growth, cytoskeletal reorganization, and the activation of protein kinases. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]
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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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAC1 | NM_006908.5 | c.107+40G>A | intron_variant | ENST00000348035.9 | NP_008839.2 | |||
RAC1 | NM_018890.4 | c.107+40G>A | intron_variant | NP_061485.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAC1 | ENST00000348035.9 | c.107+40G>A | intron_variant | 1 | NM_006908.5 | ENSP00000258737 | P1 |
Frequencies
GnomAD3 genomes AF: 0.168 AC: 25547AN: 151990Hom.: 2516 Cov.: 32
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GnomAD3 exomes AF: 0.182 AC: 36771AN: 202566Hom.: 3742 AF XY: 0.182 AC XY: 20222AN XY: 111162
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GnomAD4 exome AF: 0.216 AC: 256593AN: 1188826Hom.: 29462 Cov.: 16 AF XY: 0.213 AC XY: 128342AN XY: 602698
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GnomAD4 genome AF: 0.168 AC: 25550AN: 152108Hom.: 2516 Cov.: 32 AF XY: 0.165 AC XY: 12262AN XY: 74352
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at