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GeneBe

19-1440091-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001018.5(RPS15):c.162C>T(p.His54=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000213 in 1,583,426 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00020 ( 0 hom. )

Consequence

RPS15
NM_001018.5 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.54
Variant links:
Genes affected
RPS15 (HGNC:10388): (ribosomal protein S15) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S19P family of ribosomal proteins. It is located in the cytoplasm. This gene has been found to be activated in various tumors, such as insulinomas, esophageal cancers, and colon cancers. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant 19-1440091-C-T is Benign according to our data. Variant chr19-1440091-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3048640.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.54 with no splicing effect.
BS2
High AC in GnomAd at 51 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPS15NM_001018.5 linkuse as main transcriptc.162C>T p.His54= synonymous_variant 3/4 ENST00000592588.7
RPS15NM_001308226.2 linkuse as main transcriptc.183C>T p.His61= synonymous_variant 3/4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPS15ENST00000592588.7 linkuse as main transcriptc.162C>T p.His54= synonymous_variant 3/41 NM_001018.5 P1

Frequencies

GnomAD3 genomes
AF:
0.000335
AC:
51
AN:
152268
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000964
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00164
Gnomad ASJ
AF:
0.000864
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000250
Gnomad OTH
AF:
0.000955
GnomAD3 exomes
AF:
0.000302
AC:
58
AN:
192314
Hom.:
0
AF XY:
0.000308
AC XY:
32
AN XY:
103774
show subpopulations
Gnomad AFR exome
AF:
0.000193
Gnomad AMR exome
AF:
0.000743
Gnomad ASJ exome
AF:
0.00136
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000787
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000190
Gnomad OTH exome
AF:
0.00121
GnomAD4 exome
AF:
0.000201
AC:
287
AN:
1431158
Hom.:
0
Cov.:
33
AF XY:
0.000199
AC XY:
141
AN XY:
708634
show subpopulations
Gnomad4 AFR exome
AF:
0.000421
Gnomad4 AMR exome
AF:
0.00102
Gnomad4 ASJ exome
AF:
0.00201
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000110
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000112
Gnomad4 OTH exome
AF:
0.000640
GnomAD4 genome
AF:
0.000335
AC:
51
AN:
152268
Hom.:
0
Cov.:
32
AF XY:
0.000390
AC XY:
29
AN XY:
74392
show subpopulations
Gnomad4 AFR
AF:
0.0000964
Gnomad4 AMR
AF:
0.00164
Gnomad4 ASJ
AF:
0.000864
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000250
Gnomad4 OTH
AF:
0.000955
Alfa
AF:
0.000541
Hom.:
0
Bravo
AF:
0.000370

ClinVar

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

Submissions by phenotype

RPS15-related disorder Benign:1
Likely benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesSep 27, 2023This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.57
Cadd
Benign
10
Dann
Benign
0.90

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: rs778995103; hg19: chr19-1440090; API