2-86974160-G-A
Position:
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_001382344.1(RGPD1):c.1361G>A(p.Arg454Gln) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000030 ( 0 hom., cov: 18)
Exomes 𝑓: 0.000038 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
RGPD1
NM_001382344.1 missense
NM_001382344.1 missense
Scores
1
6
12
Clinical Significance
Conservation
PhyloP100: 4.96
Genes affected
RGPD1 (HGNC:32414): (RANBP2 like and GRIP domain containing 1) Predicted to contribute to GTPase activator activity. Predicted to be involved in NLS-bearing protein import into nucleus. Predicted to be part of nuclear pore. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.31476337).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RGPD1 | NM_001382344.1 | c.1361G>A | p.Arg454Gln | missense_variant | 10/23 | ENST00000641458.2 | NP_001369273.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RGPD1 | ENST00000641458.2 | c.1361G>A | p.Arg454Gln | missense_variant | 10/23 | NM_001382344.1 | ENSP00000492954 | A2 | ||
RGPD1 | ENST00000398193.8 | c.1361G>A | p.Arg454Gln | missense_variant | 10/23 | 1 | ENSP00000381253 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 4AN: 135118Hom.: 0 Cov.: 18 FAILED QC
GnomAD3 genomes
AF:
AC:
4
AN:
135118
Hom.:
Cov.:
18
FAILED QC
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000379 AC: 55AN: 1452090Hom.: 0 Cov.: 30 AF XY: 0.0000374 AC XY: 27AN XY: 721988
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
55
AN:
1452090
Hom.:
Cov.:
30
AF XY:
AC XY:
27
AN XY:
721988
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000296 AC: 4AN: 135118Hom.: 0 Cov.: 18 AF XY: 0.0000613 AC XY: 4AN XY: 65240
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
4
AN:
135118
Hom.:
Cov.:
18
AF XY:
AC XY:
4
AN XY:
65240
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 07, 2021 | The c.1337G>A (p.R446Q) alteration is located in exon 10 (coding exon 10) of the RGPD1 gene. This alteration results from a G to A substitution at nucleotide position 1337, causing the arginine (R) at amino acid position 446 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Pathogenic
DEOGEN2
Benign
T;.;T;.
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;.;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;M;.
MutationTaster
Benign
N;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;.
REVEL
Benign
Sift
Benign
T;T;T;.
Sift4G
Uncertain
D;D;D;.
Polyphen
1.0
.;D;.;.
Vest4
MutPred
0.41
.;Loss of loop (P = 0.0022);.;Loss of loop (P = 0.0022);
MVP
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