19-39435885-T-C
Position:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001020.6(RPS16):āc.11A>Gā(p.Lys4Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000192 in 1,606,316 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 Uncertain significance (ā ).
Frequency
Genomes: š 0.00011 ( 0 hom., cov: 34)
Exomes š: 0.00020 ( 0 hom. )
Consequence
RPS16
NM_001020.6 missense
NM_001020.6 missense
Scores
1
3
11
Clinical Significance
Conservation
PhyloP100: 6.78
Genes affected
RPS16 (HGNC:10396): (ribosomal protein S16) 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 S9P 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 Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.19945264).
BS2
?
High AC in GnomAd4 at 16 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS16 | NM_001020.6 | c.11A>G | p.Lys4Arg | missense_variant | 1/5 | ENST00000251453.8 | |
RPS16 | NM_001363860.2 | c.11A>G | p.Lys4Arg | missense_variant | 1/4 | ||
RPS16 | NM_001321111.2 | c.11A>G | p.Lys4Arg | missense_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS16 | ENST00000251453.8 | c.11A>G | p.Lys4Arg | missense_variant | 1/5 | 1 | NM_001020.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152248Hom.: 0 Cov.: 34
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000734 AC: 18AN: 245204Hom.: 0 AF XY: 0.0000600 AC XY: 8AN XY: 133232
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GnomAD4 exome AF: 0.000202 AC: 293AN: 1454068Hom.: 0 Cov.: 36 AF XY: 0.000200 AC XY: 145AN XY: 723816
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GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152248Hom.: 0 Cov.: 34 AF XY: 0.000108 AC XY: 8AN XY: 74382
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 18, 2022 | The c.11A>G (p.K4R) alteration is located in exon 1 (coding exon 1) of the RPS16 gene. This alteration results from a A to G substitution at nucleotide position 11, causing the lysine (K) at amino acid position 4 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T;T
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
Sift4G
Benign
T;T;T;T
Polyphen
0.35, 0.0
.;B;B;.
Vest4
MVP
MPC
0.77
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at