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rs836488

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006908.5(RAC1):c.35+5392C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,134 control chromosomes in the GnomAD database, including 2,555 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 0.13 ( 2555 hom., cov: 33)

Consequence

RAC1
NM_006908.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.51
Variant links:
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RAC1NM_006908.5 linkuse as main transcriptc.35+5392C>T intron_variant ENST00000348035.9
RAC1NM_018890.4 linkuse as main transcriptc.35+5392C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RAC1ENST00000348035.9 linkuse as main transcriptc.35+5392C>T intron_variant 1 NM_006908.5 P1P63000-1

Frequencies

GnomAD3 genomes
AF:
0.132
AC:
20036
AN:
152016
Hom.:
2533
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.235
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.171
Gnomad ASJ
AF:
0.0806
Gnomad EAS
AF:
0.559
Gnomad SAS
AF:
0.277
Gnomad FIN
AF:
0.0930
Gnomad MID
AF:
0.0918
Gnomad NFE
AF:
0.0286
Gnomad OTH
AF:
0.123
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.132
AC:
20097
AN:
152134
Hom.:
2555
Cov.:
33
AF XY:
0.142
AC XY:
10553
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.236
Gnomad4 AMR
AF:
0.170
Gnomad4 ASJ
AF:
0.0806
Gnomad4 EAS
AF:
0.560
Gnomad4 SAS
AF:
0.276
Gnomad4 FIN
AF:
0.0930
Gnomad4 NFE
AF:
0.0286
Gnomad4 OTH
AF:
0.131
Alfa
AF:
0.0756
Hom.:
116
Bravo
AF:
0.136
Asia WGS
AF:
0.428
AC:
1484
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
0.94
Dann
Benign
0.84

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs836488; hg19: chr7-6419793; API