16-1964288-G-A
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_002952.4(RPS2):c.255C>T(p.Ser85=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00163 in 1,612,134 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0087 ( 25 hom., cov: 34)
Exomes 𝑓: 0.00089 ( 31 hom. )
Consequence
RPS2
NM_002952.4 synonymous
NM_002952.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.191
Genes affected
RPS2 (HGNC:10404): (ribosomal protein S2) 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 S5P family of ribosomal proteins. It is located in the cytoplasm. This gene shares sequence similarity with mouse LLRep3. It is co-transcribed with the small nucleolar RNA gene U64, which is located in its third intron. 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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
?
Variant 16-1964288-G-A is Benign according to our data. Variant chr16-1964288-G-A is described in ClinVar as [Benign]. Clinvar id is 781179.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.191 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00868 (1323/152342) while in subpopulation AFR AF= 0.0302 (1255/41584). AF 95% confidence interval is 0.0288. There are 25 homozygotes in gnomad4. There are 600 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1323 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS2 | NM_002952.4 | c.255C>T | p.Ser85= | synonymous_variant | 3/7 | ENST00000343262.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS2 | ENST00000343262.9 | c.255C>T | p.Ser85= | synonymous_variant | 3/7 | 1 | NM_002952.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00863 AC: 1314AN: 152226Hom.: 24 Cov.: 34
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GnomAD3 exomes AF: 0.00229 AC: 575AN: 250946Hom.: 15 AF XY: 0.00168 AC XY: 228AN XY: 135800
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GnomAD4 exome AF: 0.000889 AC: 1298AN: 1459792Hom.: 31 Cov.: 37 AF XY: 0.000785 AC XY: 570AN XY: 726300
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GnomAD4 genome ? AF: 0.00868 AC: 1323AN: 152342Hom.: 25 Cov.: 34 AF XY: 0.00805 AC XY: 600AN XY: 74500
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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 submitter | clinical testing | Invitae | Jun 21, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at