rs10025155
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000661.5(RPL9):c.392-71A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 1,438,862 control chromosomes in the GnomAD database, including 25,383 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.21 ( 3712 hom., cov: 32)
Exomes 𝑓: 0.18 ( 21671 hom. )
Consequence
RPL9
NM_000661.5 intron
NM_000661.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.221
Genes affected
RPL9 (HGNC:10369): (ribosomal protein L9) 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 L6P 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. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
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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=-0.8).
BP6
?
Variant 4-39455015-T-C is Benign according to our data. Variant chr4-39455015-T-C is described in ClinVar as [Benign]. Clinvar id is 1273476.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPL9 | NM_000661.5 | c.392-71A>G | intron_variant | ENST00000295955.14 | |||
RPL9 | NM_001024921.4 | c.392-71A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPL9 | ENST00000295955.14 | c.392-71A>G | intron_variant | 1 | NM_000661.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.208 AC: 31686AN: 152072Hom.: 3701 Cov.: 32
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GnomAD4 exome AF: 0.180 AC: 231622AN: 1286672Hom.: 21671 Cov.: 17 AF XY: 0.180 AC XY: 115732AN XY: 644264
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GnomAD4 genome ? AF: 0.209 AC: 31742AN: 152190Hom.: 3712 Cov.: 32 AF XY: 0.203 AC XY: 15127AN XY: 74396
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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 | GeneDx | May 14, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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