13-27255173-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000982.4(RPL21):c.130-69G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.995 in 793,018 control chromosomes in the GnomAD database, including 392,799 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.98 ( 73812 hom., cov: 32)
Exomes 𝑓: 1.0 ( 318987 hom. )
Consequence
RPL21
NM_000982.4 intron
NM_000982.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.38
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 13-27255173-G-A is Benign according to our data. Variant chr13-27255173-G-A is described in ClinVar as [Benign]. Clinvar id is 1235163.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPL21 | NM_000982.4 | c.130-69G>A | intron_variant | ENST00000311549.11 | |||
SNORD102 | NR_002574.1 | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPL21 | ENST00000311549.11 | c.130-69G>A | intron_variant | 1 | NM_000982.4 | P1 | |||
SNORD102 | ENST00000384769.1 | downstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.984 AC: 149818AN: 152236Hom.: 73760 Cov.: 32
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GnomAD3 exomes AF: 0.996 AC: 248309AN: 249356Hom.: 123653 AF XY: 0.997 AC XY: 134476AN XY: 134896
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GnomAD4 exome AF: 0.998 AC: 639285AN: 640664Hom.: 318987 Cov.: 7 AF XY: 0.998 AC XY: 347836AN XY: 348424
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GnomAD4 genome ? AF: 0.984 AC: 149928AN: 152354Hom.: 73812 Cov.: 32 AF XY: 0.985 AC XY: 73361AN XY: 74502
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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 | Jul 09, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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