17-38850183-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_000978.4(RPL23):c.372G>A(p.Glu124=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,606,946 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000019 ( 0 hom. )
Consequence
RPL23
NM_000978.4 synonymous
NM_000978.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.202
Genes affected
RPL23 (HGNC:10316): (ribosomal protein L23) 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 60S subunit. The protein belongs to the L14P family of ribosomal proteins. It is located in the cytoplasm. This gene has been referred to as rpL17 because the encoded protein shares amino acid identity with ribosomal protein L17 from Saccharomyces cerevisiae; however, its official symbol is RPL23. 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 -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
?
Variant 17-38850183-C-T is Benign according to our data. Variant chr17-38850183-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2869009.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
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Synonymous conserved (PhyloP=0.202 with no splicing effect.
BS2
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High AC in GnomAdExome4 at 27 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPL23 | NM_000978.4 | c.372G>A | p.Glu124= | synonymous_variant | 5/5 | ENST00000479035.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPL23 | ENST00000479035.7 | c.372G>A | p.Glu124= | synonymous_variant | 5/5 | 1 | NM_000978.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151786Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000162 AC: 4AN: 247300Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 134120
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GnomAD4 exome AF: 0.0000186 AC: 27AN: 1455160Hom.: 0 Cov.: 30 AF XY: 0.0000221 AC XY: 16AN XY: 723744
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GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151786Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74094
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 30, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at