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2-55235327-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.322-101A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00484 in 1,311,332 control chromosomes in the GnomAD database, including 239 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.023 ( 125 hom., cov: 32)
Exomes 𝑓: 0.0025 ( 114 hom. )

Consequence

RPS27A
NM_002954.6 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.44
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=-0.82).
BP6
Variant 2-55235327-A-T is Benign according to our data. Variant chr2-55235327-A-T is described in ClinVar as [Benign]. Clinvar id is 1231269.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0771 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPS27ANM_002954.6 linkuse as main transcriptc.322-101A>T intron_variant ENST00000272317.11
RPS27ANM_001135592.2 linkuse as main transcriptc.322-101A>T intron_variant
RPS27ANM_001177413.1 linkuse as main transcriptc.322-101A>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPS27AENST00000272317.11 linkuse as main transcriptc.322-101A>T intron_variant 1 NM_002954.6 P1
RPS27AENST00000404735.1 linkuse as main transcriptc.322-101A>T intron_variant 1 P1
RPS27AENST00000402285.7 linkuse as main transcriptc.322-101A>T intron_variant 3 P1
RPS27AENST00000495843.1 linkuse as main transcriptn.978-101A>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.0227
AC:
3451
AN:
152232
Hom.:
124
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0792
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00713
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.000191
Gnomad OTH
AF:
0.0181
GnomAD4 exome
AF:
0.00248
AC:
2878
AN:
1158982
Hom.:
114
Cov.:
16
AF XY:
0.00213
AC XY:
1256
AN XY:
590944
show subpopulations
Gnomad4 AFR exome
AF:
0.0878
Gnomad4 AMR exome
AF:
0.00344
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000876
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000497
Gnomad4 OTH exome
AF:
0.00505
GnomAD4 genome
AF:
0.0227
AC:
3464
AN:
152350
Hom.:
125
Cov.:
32
AF XY:
0.0219
AC XY:
1629
AN XY:
74508
show subpopulations
Gnomad4 AFR
AF:
0.0793
Gnomad4 AMR
AF:
0.00712
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000621
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000191
Gnomad4 OTH
AF:
0.0180
Alfa
AF:
0.0173
Hom.:
10
Bravo
AF:
0.0260
Asia WGS
AF:
0.00404
AC:
15
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
-0.82
Cadd
Benign
5.8
Dann
Benign
0.60

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: rs72918921; hg19: chr2-55462463; API