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2-55234273-T-C

Variant summary

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

The NM_002954.6(RPS27A):c.189+69T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0148 in 1,147,760 control chromosomes in the GnomAD database, including 1,511 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.061 ( 906 hom., cov: 32)
Exomes 𝑓: 0.0078 ( 605 hom. )

Consequence

RPS27A
NM_002954.6 intron

Scores

7

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.504
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 (MetaRNN=0.0018050075).
BP6
Variant 2-55234273-T-C is Benign according to our data. Variant chr2-55234273-T-C is described in ClinVar as [Benign]. Clinvar id is 1242743.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPS27ANM_002954.6 linkuse as main transcriptc.189+69T>C intron_variant ENST00000272317.11
RPS27ANM_001135592.2 linkuse as main transcriptc.189+69T>C intron_variant
RPS27ANM_001177413.1 linkuse as main transcriptc.189+69T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPS27AENST00000272317.11 linkuse as main transcriptc.189+69T>C intron_variant 1 NM_002954.6 P1

Frequencies

GnomAD3 genomes
AF:
0.0608
AC:
9242
AN:
152126
Hom.:
908
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.205
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0317
Gnomad ASJ
AF:
0.0211
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00104
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.00168
Gnomad OTH
AF:
0.0435
GnomAD4 exome
AF:
0.00782
AC:
7786
AN:
995518
Hom.:
605
Cov.:
13
AF XY:
0.00681
AC XY:
3502
AN XY:
513984
show subpopulations
Gnomad4 AFR exome
AF:
0.210
Gnomad4 AMR exome
AF:
0.0147
Gnomad4 ASJ exome
AF:
0.0224
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000254
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00121
Gnomad4 OTH exome
AF:
0.0187
GnomAD4 genome
AF:
0.0607
AC:
9247
AN:
152242
Hom.:
906
Cov.:
32
AF XY:
0.0582
AC XY:
4334
AN XY:
74426
show subpopulations
Gnomad4 AFR
AF:
0.204
Gnomad4 AMR
AF:
0.0316
Gnomad4 ASJ
AF:
0.0211
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000622
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00166
Gnomad4 OTH
AF:
0.0431
Alfa
AF:
0.0388
Hom.:
86
Bravo
AF:
0.0711
TwinsUK
AF:
0.00162
AC:
6
ALSPAC
AF:
0.000519
AC:
2

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 16, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
Cadd
Benign
4.9
Dann
Benign
0.85
DEOGEN2
Benign
0.011
T
FATHMM_MKL
Benign
0.053
N
LIST_S2
Benign
0.20
T
MetaRNN
Benign
0.0018
T
MutationTaster
Benign
0.92
P;P;P
GERP RS
1.4
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs74478570; hg19: chr2-55461409; API