13-27253852-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000982.4(RPL21):c.67+9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00301 in 1,519,836 control chromosomes in the GnomAD database, including 112 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.016 ( 67 hom., cov: 33)
Exomes 𝑓: 0.0016 ( 45 hom. )
Consequence
RPL21
NM_000982.4 intron
NM_000982.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.759
Genes affected
RPL21 (HGNC:10313): (ribosomal protein L21) 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 L21E 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 Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
Variant 13-27253852-G-A is Benign according to our data. Variant chr13-27253852-G-A is described in ClinVar as [Benign]. Clinvar id is 1270905.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0519 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPL21 | NM_000982.4 | c.67+9G>A | intron_variant | ENST00000311549.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPL21 | ENST00000311549.11 | c.67+9G>A | intron_variant | 1 | NM_000982.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0156 AC: 2378AN: 152190Hom.: 67 Cov.: 33
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GnomAD3 exomes AF: 0.00409 AC: 1028AN: 251168Hom.: 28 AF XY: 0.00278 AC XY: 378AN XY: 135752
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GnomAD4 exome AF: 0.00160 AC: 2184AN: 1367528Hom.: 45 Cov.: 22 AF XY: 0.00133 AC XY: 913AN XY: 685806
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GnomAD4 genome AF: 0.0157 AC: 2387AN: 152308Hom.: 67 Cov.: 33 AF XY: 0.0150 AC XY: 1120AN XY: 74484
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 04, 2020 | - - |
Computational scores
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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