rs915942
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1
The NM_006013.5(RPL10):c.-24+3G>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 886,049 control chromosomes in the GnomAD database, including 6,838 homozygotes. There are 35,176 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.18 ( 1814 hom., 6157 hem., cov: 25)
Exomes 𝑓: 0.13 ( 5024 hom. 29019 hem. )
Consequence
RPL10
NM_006013.5 splice_donor_region, intron
NM_006013.5 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.0003592
2
Clinical Significance
Conservation
PhyloP100: 2.95
Genes affected
RPL10 (HGNC:10298): (ribosomal protein L10) This gene encodes a ribosomal protein that is a component of the 60S ribosome subunit. The related protein in chicken can bind to c-Jun and can repress c-Jun-mediated transcriptional activation. Some studies have detected an association between variation in this gene and autism spectrum disorders, though others do not detect this relationship. There are multiple pseudogenes of this gene dispersed throughout the genome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BP6
?
Variant X-154398397-G-A is Benign according to our data. Variant chrX-154398397-G-A is described in ClinVar as [Benign]. Clinvar id is 1327969.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPL10 | NM_006013.5 | c.-24+3G>A | splice_donor_region_variant, intron_variant | ENST00000369817.7 | |||
LOC124905228 | XR_007068356.1 | n.446C>T | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPL10 | ENST00000369817.7 | c.-24+3G>A | splice_donor_region_variant, intron_variant | 5 | NM_006013.5 | P1 | |||
ENST00000624054.2 | n.446C>T | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.180 AC: 20347AN: 112892Hom.: 1802 Cov.: 25 AF XY: 0.175 AC XY: 6125AN XY: 35062
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GnomAD3 exomes AF: 0.144 AC: 25761AN: 179374Hom.: 1588 AF XY: 0.136 AC XY: 8947AN XY: 65634
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GnomAD4 exome AF: 0.127 AC: 97883AN: 773104Hom.: 5024 Cov.: 13 AF XY: 0.130 AC XY: 29019AN XY: 223062
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GnomAD4 genome ? AF: 0.181 AC: 20407AN: 112945Hom.: 1814 Cov.: 25 AF XY: 0.175 AC XY: 6157AN XY: 35125
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Intellectual disability, X-linked, syndromic, 35 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at