2-101002915-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000993.5(RPL31):c.107+107C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 782,068 control chromosomes in the GnomAD database, including 6,213 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.10 ( 977 hom., cov: 32)
Exomes 𝑓: 0.12 ( 5236 hom. )
Consequence
RPL31
NM_000993.5 intron
NM_000993.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.107
Genes affected
RPL31 (HGNC:10334): (ribosomal protein L31) 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 L31E family of ribosomal proteins. It is located in the cytoplasm. Higher levels of expression of this gene in familial adenomatous polyps compared to matched normal tissues have been observed. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [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=-0.79).
BP6
Variant 2-101002915-C-T is Benign according to our data. Variant chr2-101002915-C-T is described in ClinVar as [Benign]. Clinvar id is 1291849.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPL31 | NM_000993.5 | c.107+107C>T | intron_variant | ENST00000264258.8 | |||
RPL31 | NM_001098577.3 | c.107+107C>T | intron_variant | ||||
RPL31 | NM_001099693.2 | c.107+107C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPL31 | ENST00000264258.8 | c.107+107C>T | intron_variant | 1 | NM_000993.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.103 AC: 15638AN: 152002Hom.: 977 Cov.: 32
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GnomAD4 exome AF: 0.119 AC: 75136AN: 629946Hom.: 5236 AF XY: 0.117 AC XY: 38995AN XY: 332390
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GnomAD4 genome AF: 0.103 AC: 15641AN: 152122Hom.: 977 Cov.: 32 AF XY: 0.103 AC XY: 7642AN XY: 74356
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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 | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 17, 2021 | - - |
Computational scores
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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