16-1964488-T-C
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_002952.4(RPS2):āc.138A>Gā(p.Arg46=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00399 in 1,607,308 control chromosomes in the GnomAD database, including 251 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.021 ( 137 hom., cov: 34)
Exomes š: 0.0022 ( 114 hom. )
Consequence
RPS2
NM_002952.4 synonymous
NM_002952.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.560
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=-0.62).
BP6
?
Variant 16-1964488-T-C is Benign according to our data. Variant chr16-1964488-T-C is described in ClinVar as [Benign]. Clinvar id is 768738.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
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Synonymous conserved (PhyloP=-0.56 with no splicing effect.
BA1
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GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0729 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS2 | NM_002952.4 | c.138A>G | p.Arg46= | synonymous_variant | 2/7 | ENST00000343262.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS2 | ENST00000343262.9 | c.138A>G | p.Arg46= | synonymous_variant | 2/7 | 1 | NM_002952.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0214 AC: 3262AN: 152084Hom.: 136 Cov.: 34
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GnomAD3 exomes AF: 0.00507 AC: 1187AN: 234104Hom.: 45 AF XY: 0.00390 AC XY: 503AN XY: 129132
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GnomAD4 exome AF: 0.00216 AC: 3143AN: 1455106Hom.: 114 Cov.: 33 AF XY: 0.00181 AC XY: 1311AN XY: 723754
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GnomAD4 genome ? AF: 0.0215 AC: 3271AN: 152202Hom.: 137 Cov.: 34 AF XY: 0.0205 AC XY: 1523AN XY: 74416
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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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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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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