2-101004144-T-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000993.5(RPL31):c.108-14T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000676 in 1,612,426 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 0.00015 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000059 ( 0 hom. )
Consequence
RPL31
NM_000993.5 splice_polypyrimidine_tract, intron
NM_000993.5 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.64
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
Variant 2-101004144-T-C is Benign according to our data. Variant chr2-101004144-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2864615.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 23 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPL31 | NM_000993.5 | c.108-14T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000264258.8 | |||
RPL31 | NM_001098577.3 | c.108-14T>C | splice_polypyrimidine_tract_variant, intron_variant | ||||
RPL31 | NM_001099693.2 | c.108-14T>C | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPL31 | ENST00000264258.8 | c.108-14T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000993.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152210Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000124 AC: 31AN: 249426Hom.: 0 AF XY: 0.000141 AC XY: 19AN XY: 134840
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GnomAD4 exome AF: 0.0000589 AC: 86AN: 1460098Hom.: 0 Cov.: 31 AF XY: 0.0000675 AC XY: 49AN XY: 726304
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GnomAD4 genome AF: 0.000151 AC: 23AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74492
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Sep 24, 2023 | - - |
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