2-55233475-AGGT-A
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_002954.6(RPS27A):c.103+60_103+62delGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00784 in 1,221,246 control chromosomes in the GnomAD database, including 459 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.034 ( 277 hom., cov: 33)
Exomes 𝑓: 0.0042 ( 182 hom. )
Consequence
RPS27A
NM_002954.6 intron
NM_002954.6 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.56
Genes affected
RPS27A (HGNC:10417): (ribosomal protein S27a) Ubiquitin, a highly conserved protein that has a major role in targeting cellular proteins for degradation by the 26S proteosome, is synthesized as a precursor protein consisting of either polyubiquitin chains or a single ubiquitin fused to an unrelated protein. This gene encodes a fusion protein consisting of ubiquitin at the N terminus and ribosomal protein S27a at the C terminus. When expressed in yeast, the protein is post-translationally processed, generating free ubiquitin monomer and ribosomal protein S27a. Ribosomal protein S27a is a component of the 40S subunit of the ribosome and belongs to the S27AE family of ribosomal proteins. It contains C4-type zinc finger domains and is located in the cytoplasm. Pseudogenes derived from this gene are present in the genome. As with ribosomal protein S27a, ribosomal protein L40 is also synthesized as a fusion protein with ubiquitin; similarly, ribosomal protein S30 is synthesized as a fusion protein with the ubiquitin-like protein fubi. Multiple alternatively spliced transcript variants that encode the same proteins have been identified.[provided by RefSeq, Sep 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP6
Variant 2-55233475-AGGT-A is Benign according to our data. Variant chr2-55233475-AGGT-A is described in ClinVar as [Benign]. Clinvar id is 1253611.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPS27A | NM_002954.6 | c.103+60_103+62delGTG | intron_variant | Intron 3 of 5 | ENST00000272317.11 | NP_002945.1 | ||
RPS27A | NM_001135592.2 | c.103+60_103+62delGTG | intron_variant | Intron 3 of 5 | NP_001129064.1 | |||
RPS27A | NM_001177413.1 | c.103+60_103+62delGTG | intron_variant | Intron 2 of 4 | NP_001170884.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0336 AC: 5113AN: 152146Hom.: 277 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
5113
AN:
152146
Hom.:
Cov.:
33
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 AF: 0.00417 AC: 4461AN: 1068982Hom.: 182 AF XY: 0.00352 AC XY: 1935AN XY: 549396 show subpopulations
GnomAD4 exome
AF:
AC:
4461
AN:
1068982
Hom.:
AF XY:
AC XY:
1935
AN XY:
549396
Gnomad4 AFR exome
AF:
AC:
3161
AN:
25946
Gnomad4 AMR exome
AF:
AC:
354
AN:
43142
Gnomad4 ASJ exome
AF:
AC:
6
AN:
23662
Gnomad4 EAS exome
AF:
AC:
0
AN:
37676
Gnomad4 SAS exome
AF:
AC:
9
AN:
77412
Gnomad4 FIN exome
AF:
AC:
0
AN:
52846
Gnomad4 NFE exome
AF:
AC:
445
AN:
757426
Gnomad4 Remaining exome
AF:
AC:
450
AN:
47310
Heterozygous variant carriers
0
224
448
672
896
1120
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
96
192
288
384
480
<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: 0.0336 AC: 5115AN: 152264Hom.: 277 Cov.: 33 AF XY: 0.0320 AC XY: 2384AN XY: 74458 show subpopulations
GnomAD4 genome
AF:
AC:
5115
AN:
152264
Hom.:
Cov.:
33
AF XY:
AC XY:
2384
AN XY:
74458
Gnomad4 AFR
AF:
AC:
0.113287
AN:
0.113287
Gnomad4 AMR
AF:
AC:
0.0184314
AN:
0.0184314
Gnomad4 ASJ
AF:
AC:
0
AN:
0
Gnomad4 EAS
AF:
AC:
0
AN:
0
Gnomad4 SAS
AF:
AC:
0.000413907
AN:
0.000413907
Gnomad4 FIN
AF:
AC:
0
AN:
0
Gnomad4 NFE
AF:
AC:
0.000940706
AN:
0.000940706
Gnomad4 OTH
AF:
AC:
0.0294118
AN:
0.0294118
Heterozygous variant carriers
0
241
481
722
962
1203
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
52
104
156
208
260
<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.:
Asia WGS
AF:
AC:
22
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
May 16, 2021
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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