chr7-6374750-G-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_006908.5(RAC1):c.15G>A(p.Lys5Lys) variant causes a synonymous change. The variant allele was found at a frequency of 0.000001 in 998,912 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000010 ( 0 hom. )
Consequence
RAC1
NM_006908.5 synonymous
NM_006908.5 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 4.02
Publications
0 publications found
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]
RAC1 Gene-Disease associations (from GenCC):
- intellectual disability, autosomal dominant 48Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Illumina, Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 7-6374750-G-A is Benign according to our data. Variant chr7-6374750-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3339089.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000100 AC: 1AN: 998912Hom.: 0 Cov.: 30 AF XY: 0.00000208 AC XY: 1AN XY: 479742 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1
AN:
998912
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
479742
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
19048
American (AMR)
AF:
AC:
0
AN:
7200
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
10590
East Asian (EAS)
AF:
AC:
0
AN:
14912
South Asian (SAS)
AF:
AC:
0
AN:
26308
European-Finnish (FIN)
AF:
AC:
0
AN:
21816
Middle Eastern (MID)
AF:
AC:
0
AN:
3268
European-Non Finnish (NFE)
AF:
AC:
1
AN:
859852
Other (OTH)
AF:
AC:
0
AN:
35918
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Jul 08, 2024
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Uncertain
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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