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2-55233469-A-T

Variant summary

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

The NM_002954.6(RPS27A):c.103+52A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 1,341,404 control chromosomes in the GnomAD database, including 387,529 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.76 ( 44256 hom., cov: 32)
Exomes 𝑓: 0.76 ( 343273 hom. )

Consequence

RPS27A
NM_002954.6 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.63
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=-0.88).
BP6
Variant 2-55233469-A-T is Benign according to our data. Variant chr2-55233469-A-T is described in ClinVar as [Benign]. Clinvar id is 1238560.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPS27ANM_002954.6 linkuse as main transcriptc.103+52A>T intron_variant ENST00000272317.11
RPS27ANM_001135592.2 linkuse as main transcriptc.103+52A>T intron_variant
RPS27ANM_001177413.1 linkuse as main transcriptc.103+52A>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPS27AENST00000272317.11 linkuse as main transcriptc.103+52A>T intron_variant 1 NM_002954.6 P1

Frequencies

GnomAD3 genomes
AF:
0.761
AC:
115713
AN:
151954
Hom.:
44220
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.765
Gnomad AMI
AF:
0.862
Gnomad AMR
AF:
0.741
Gnomad ASJ
AF:
0.655
Gnomad EAS
AF:
0.627
Gnomad SAS
AF:
0.659
Gnomad FIN
AF:
0.844
Gnomad MID
AF:
0.658
Gnomad NFE
AF:
0.773
Gnomad OTH
AF:
0.760
GnomAD3 exomes
AF:
0.741
AC:
178080
AN:
240220
Hom.:
66104
AF XY:
0.740
AC XY:
96316
AN XY:
130150
show subpopulations
Gnomad AFR exome
AF:
0.764
Gnomad AMR exome
AF:
0.714
Gnomad ASJ exome
AF:
0.666
Gnomad EAS exome
AF:
0.642
Gnomad SAS exome
AF:
0.680
Gnomad FIN exome
AF:
0.841
Gnomad NFE exome
AF:
0.767
Gnomad OTH exome
AF:
0.741
GnomAD4 exome
AF:
0.758
AC:
902075
AN:
1189332
Hom.:
343273
Cov.:
16
AF XY:
0.757
AC XY:
457708
AN XY:
604954
show subpopulations
Gnomad4 AFR exome
AF:
0.761
Gnomad4 AMR exome
AF:
0.717
Gnomad4 ASJ exome
AF:
0.663
Gnomad4 EAS exome
AF:
0.618
Gnomad4 SAS exome
AF:
0.683
Gnomad4 FIN exome
AF:
0.840
Gnomad4 NFE exome
AF:
0.773
Gnomad4 OTH exome
AF:
0.745
GnomAD4 genome
AF:
0.761
AC:
115800
AN:
152072
Hom.:
44256
Cov.:
32
AF XY:
0.761
AC XY:
56552
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.765
Gnomad4 AMR
AF:
0.741
Gnomad4 ASJ
AF:
0.655
Gnomad4 EAS
AF:
0.627
Gnomad4 SAS
AF:
0.658
Gnomad4 FIN
AF:
0.844
Gnomad4 NFE
AF:
0.773
Gnomad4 OTH
AF:
0.763
Alfa
AF:
0.724
Hom.:
4498
Bravo
AF:
0.756
Asia WGS
AF:
0.667
AC:
2320
AN:
3478

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 14, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
Cadd
Benign
0.30
Dann
Benign
0.41
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.3

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs6737227; hg19: chr2-55460605; API