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GeneBe

2-55234855-A-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_002954.6(RPS27A):c.214A>C(p.Arg72=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00284 in 1,612,484 control chromosomes in the GnomAD database, including 129 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.015 ( 57 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 72 hom. )

Consequence

RPS27A
NM_002954.6 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 5.05
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 2-55234855-A-C is Benign according to our data. Variant chr2-55234855-A-C is described in ClinVar as [Benign]. Clinvar id is 1244836.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0567 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPS27ANM_002954.6 linkuse as main transcriptc.214A>C p.Arg72= synonymous_variant 5/6 ENST00000272317.11
RPS27ANM_001135592.2 linkuse as main transcriptc.214A>C p.Arg72= synonymous_variant 5/6
RPS27ANM_001177413.1 linkuse as main transcriptc.214A>C p.Arg72= synonymous_variant 4/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPS27AENST00000272317.11 linkuse as main transcriptc.214A>C p.Arg72= synonymous_variant 5/61 NM_002954.6 P1

Frequencies

GnomAD3 genomes
AF:
0.0145
AC:
2209
AN:
152148
Hom.:
56
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0508
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00425
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000622
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000118
Gnomad OTH
AF:
0.0120
GnomAD3 exomes
AF:
0.00368
AC:
924
AN:
251082
Hom.:
22
AF XY:
0.00261
AC XY:
354
AN XY:
135772
show subpopulations
Gnomad AFR exome
AF:
0.0505
Gnomad AMR exome
AF:
0.00237
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000654
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000106
Gnomad OTH exome
AF:
0.00147
GnomAD4 exome
AF:
0.00161
AC:
2352
AN:
1460218
Hom.:
72
Cov.:
31
AF XY:
0.00139
AC XY:
1013
AN XY:
726432
show subpopulations
Gnomad4 AFR exome
AF:
0.0588
Gnomad4 AMR exome
AF:
0.00250
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000580
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000333
Gnomad4 OTH exome
AF:
0.00363
GnomAD4 genome
AF:
0.0146
AC:
2222
AN:
152266
Hom.:
57
Cov.:
32
AF XY:
0.0138
AC XY:
1024
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.0510
Gnomad4 AMR
AF:
0.00425
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000622
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000118
Gnomad4 OTH
AF:
0.0118
Alfa
AF:
0.00412
Hom.:
4
Bravo
AF:
0.0170
Asia WGS
AF:
0.00289
AC:
10
AN:
3478
EpiCase
AF:
0.000164
EpiControl
AF:
0.000178

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxMay 04, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
Cadd
Benign
12
Dann
Benign
0.91
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2230613; hg19: chr2-55461991; API