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16-18788293-C-A

Variant summary

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

The NM_001019.5(RPS15A):c.134-151G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0688 in 604,128 control chromosomes in the GnomAD database, including 1,805 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.087 ( 695 hom., cov: 32)
Exomes 𝑓: 0.063 ( 1110 hom. )

Consequence

RPS15A
NM_001019.5 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.213
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]

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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 16-18788293-C-A is Benign according to our data. Variant chr16-18788293-C-A is described in ClinVar as [Benign]. Clinvar id is 1259635.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPS15ANM_001019.5 linkuse as main transcriptc.134-151G>T intron_variant ENST00000322989.8
RPS15ANM_001030009.2 linkuse as main transcriptc.134-151G>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPS15AENST00000322989.8 linkuse as main transcriptc.134-151G>T intron_variant 1 NM_001019.5 P1

Frequencies

GnomAD3 genomes
AF:
0.0870
AC:
13241
AN:
152136
Hom.:
694
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.153
Gnomad AMI
AF:
0.0691
Gnomad AMR
AF:
0.0558
Gnomad ASJ
AF:
0.0910
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.0307
Gnomad FIN
AF:
0.0432
Gnomad MID
AF:
0.0791
Gnomad NFE
AF:
0.0719
Gnomad OTH
AF:
0.0798
GnomAD4 exome
AF:
0.0626
AC:
28296
AN:
451874
Hom.:
1110
AF XY:
0.0609
AC XY:
14619
AN XY:
240214
show subpopulations
Gnomad4 AFR exome
AF:
0.148
Gnomad4 AMR exome
AF:
0.0479
Gnomad4 ASJ exome
AF:
0.0929
Gnomad4 EAS exome
AF:
0.0000648
Gnomad4 SAS exome
AF:
0.0344
Gnomad4 FIN exome
AF:
0.0504
Gnomad4 NFE exome
AF:
0.0705
Gnomad4 OTH exome
AF:
0.0689
GnomAD4 genome
AF:
0.0870
AC:
13251
AN:
152254
Hom.:
695
Cov.:
32
AF XY:
0.0841
AC XY:
6259
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.152
Gnomad4 AMR
AF:
0.0557
Gnomad4 ASJ
AF:
0.0910
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.0307
Gnomad4 FIN
AF:
0.0432
Gnomad4 NFE
AF:
0.0719
Gnomad4 OTH
AF:
0.0789
Alfa
AF:
0.0734
Hom.:
526
Bravo
AF:
0.0906
Asia WGS
AF:
0.0220
AC:
76
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
1.2
Dann
Benign
0.51

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: rs2641892; hg19: chr16-18799615; API