rs765113503
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_014470.4(RND1):c.11G>T(p.Arg4Ile) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
RND1
NM_014470.4 missense
NM_014470.4 missense
Scores
3
8
7
Clinical Significance
Conservation
PhyloP100: 3.60
Publications
0 publications found
Genes affected
RND1 (HGNC:18314): (Rho family GTPase 1) This gene encodes a protein that belongs to the Rho GTPase family. Members of this family regulate the organization of the actin cytoskeleton in response to extracellular growth factors. A similar protein in rat interacts with a microtubule regulator to control axon extension. [provided by RefSeq, Apr 2014]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_014470.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| RND1 | TSL:1 MANE Select | c.11G>T | p.Arg4Ile | missense | Exon 1 of 5 | ENSP00000308461.5 | Q92730 | ||
| RND1 | TSL:3 | n.11G>T | non_coding_transcript_exon | Exon 1 of 4 | ENSP00000449045.1 | F8VXU4 | |||
| RND1 | n.114G>T | non_coding_transcript_exon | Exon 1 of 4 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD2 exomes AF: 0.00000408 AC: 1AN: 245380 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
245380
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1450234Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 719500
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1450234
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
719500
African (AFR)
AF:
AC:
0
AN:
33272
American (AMR)
AF:
AC:
0
AN:
44286
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25648
East Asian (EAS)
AF:
AC:
0
AN:
39372
South Asian (SAS)
AF:
AC:
0
AN:
85278
European-Finnish (FIN)
AF:
AC:
0
AN:
53100
Middle Eastern (MID)
AF:
AC:
0
AN:
5716
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1103722
Other (OTH)
AF:
AC:
0
AN:
59840
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
Bravo
AF:
ExAC
AF:
AC:
1
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D
M_CAP
Benign
T
MetaRNN
Uncertain
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Gain of catalytic residue at Q8 (P = 0.0042)
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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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