5-82276365-G-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001025.5(RPS23):c.285+33C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 1,612,502 control chromosomes in the GnomAD database, including 275,407 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.49 ( 21220 hom., cov: 32)
Exomes 𝑓: 0.58 ( 254187 hom. )
Consequence
RPS23
NM_001025.5 intron
NM_001025.5 intron
Scores
1
14
Clinical Significance
Conservation
PhyloP100: -1.55
Genes affected
RPS23 (HGNC:10410): (ribosomal protein S23) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S12P family of ribosomal proteins. It is located in the cytoplasm. The protein shares significant amino acid similarity with S. cerevisiae ribosomal protein S28. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]
ATG10 (HGNC:20315): (autophagy related 10) Autophagy is a process for the bulk degradation of cytosolic compartments by lysosomes. ATG10 is an E2-like enzyme involved in 2 ubiquitin-like modifications essential for autophagosome formation: ATG12 (MIM 609608)-ATG5 (MIM 604261) conjugation and modification of a soluble form of MAP-LC3 (MAP1LC3A; MIM 601242), a homolog of yeast Apg8, to a membrane-bound form (Nemoto et al., 2003 [PubMed 12890687]).[supplied by OMIM, Mar 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=8.987969E-7).
BP6
Variant 5-82276365-G-C is Benign according to our data. Variant chr5-82276365-G-C is described in ClinVar as [Benign]. Clinvar id is 1327972.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.486 AC: 73832AN: 151898Hom.: 21198 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
73832
AN:
151898
Hom.:
Cov.:
32
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:
GnomAD2 exomes AF: 0.607 AC: 150284AN: 247446 AF XY: 0.608 show subpopulations
GnomAD2 exomes
AF:
AC:
150284
AN:
247446
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 AF: 0.581 AC: 849007AN: 1460486Hom.: 254187 Cov.: 42 AF XY: 0.585 AC XY: 424702AN XY: 726482 show subpopulations
GnomAD4 exome
AF:
AC:
849007
AN:
1460486
Hom.:
Cov.:
42
AF XY:
AC XY:
424702
AN XY:
726482
Gnomad4 AFR exome
AF:
AC:
5227
AN:
33476
Gnomad4 AMR exome
AF:
AC:
33456
AN:
44586
Gnomad4 ASJ exome
AF:
AC:
13435
AN:
26124
Gnomad4 EAS exome
AF:
AC:
37103
AN:
39690
Gnomad4 SAS exome
AF:
AC:
56744
AN:
86206
Gnomad4 FIN exome
AF:
AC:
31327
AN:
53350
Gnomad4 NFE exome
AF:
AC:
634684
AN:
1110958
Gnomad4 Remaining exome
AF:
AC:
34008
AN:
60338
Heterozygous variant carriers
0
18374
36748
55123
73497
91871
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
17576
35152
52728
70304
87880
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.486 AC: 73870AN: 152016Hom.: 21220 Cov.: 32 AF XY: 0.495 AC XY: 36775AN XY: 74288 show subpopulations
GnomAD4 genome
AF:
AC:
73870
AN:
152016
Hom.:
Cov.:
32
AF XY:
AC XY:
36775
AN XY:
74288
Gnomad4 AFR
AF:
AC:
0.174249
AN:
0.174249
Gnomad4 AMR
AF:
AC:
0.647602
AN:
0.647602
Gnomad4 ASJ
AF:
AC:
0.520185
AN:
0.520185
Gnomad4 EAS
AF:
AC:
0.906455
AN:
0.906455
Gnomad4 SAS
AF:
AC:
0.674969
AN:
0.674969
Gnomad4 FIN
AF:
AC:
0.589763
AN:
0.589763
Gnomad4 NFE
AF:
AC:
0.576664
AN:
0.576664
Gnomad4 OTH
AF:
AC:
0.513258
AN:
0.513258
Heterozygous variant carriers
0
1641
3282
4924
6565
8206
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
648
1296
1944
2592
3240
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
2134
ALSPAC
AF:
AC:
2145
ESP6500AA
AF:
AC:
656
ESP6500EA
AF:
AC:
4715
ExAC
AF:
AC:
72102
Asia WGS
AF:
AC:
2617
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Brachycephaly, trichomegaly, and developmental delay Benign:1
Nov 07, 2021
Genome-Nilou Lab
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Benign
T
Vest4
MutPred
Gain of glycosylation at P111 (P = 0.2225);
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Mutation Taster
=100/0
polymorphism (auto)
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