Menu
GeneBe

16-18789316-G-C

Variant summary

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

The NM_001019.5(RPS15A):c.-5-198C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0653 in 152,212 control chromosomes in the GnomAD database, including 1,080 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.065 ( 1080 hom., cov: 32)

Consequence

RPS15A
NM_001019.5 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.759
Variant links:
Genes affected
RPS15A (HGNC:10389): (ribosomal protein S15a) 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 S8P family of ribosomal proteins. It is located in the cytoplasm. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

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 16-18789316-G-C is Benign according to our data. Variant chr16-18789316-G-C is described in ClinVar as [Benign]. Clinvar id is 1290255.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPS15ANM_001019.5 linkuse as main transcriptc.-5-198C>G intron_variant ENST00000322989.8
RPS15ANM_001030009.2 linkuse as main transcriptc.-5-198C>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPS15AENST00000322989.8 linkuse as main transcriptc.-5-198C>G intron_variant 1 NM_001019.5 P1

Frequencies

GnomAD3 genomes
AF:
0.0652
AC:
9915
AN:
152094
Hom.:
1079
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.225
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0259
Gnomad ASJ
AF:
0.00692
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000830
Gnomad FIN
AF:
0.000189
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.00147
Gnomad OTH
AF:
0.0454
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0653
AC:
9932
AN:
152212
Hom.:
1080
Cov.:
32
AF XY:
0.0630
AC XY:
4690
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.224
Gnomad4 AMR
AF:
0.0258
Gnomad4 ASJ
AF:
0.00692
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000623
Gnomad4 FIN
AF:
0.000189
Gnomad4 NFE
AF:
0.00147
Gnomad4 OTH
AF:
0.0449
Alfa
AF:
0.0544
Hom.:
92
Bravo
AF:
0.0755
Asia WGS
AF:
0.0160
AC:
56
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 16, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
Cadd
Benign
0.60
Dann
Benign
0.51

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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: rs73541341; hg19: chr16-18800638; API