6-42885977-T-G
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001366481.3(RPL7L1):āc.453T>Gā(p.Phe151Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000024 in 1,585,404 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 Uncertain significance (ā ).
Frequency
Genomes: š 0.00015 ( 0 hom., cov: 31)
Exomes š: 0.000010 ( 0 hom. )
Consequence
RPL7L1
NM_001366481.3 missense
NM_001366481.3 missense
Scores
1
5
8
Clinical Significance
Conservation
PhyloP100: 0.278
Genes affected
RPL7L1 (HGNC:21370): (ribosomal protein L7 like 1) Enables RNA binding activity. Predicted to be involved in maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to act upstream of or within blastocyst formation. Predicted to be located in nucleolus. Predicted to be part of cytosolic large ribosomal subunit. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.22452608).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPL7L1 | NM_001366481.3 | c.453T>G | p.Phe151Leu | missense_variant | 5/6 | ENST00000493763.7 | NP_001353410.1 | |
RPL7L1 | NM_198486.5 | c.453T>G | p.Phe151Leu | missense_variant | 5/7 | NP_940888.3 | ||
RPL7L1 | NR_134562.3 | n.864T>G | non_coding_transcript_exon_variant | 5/7 | ||||
RPL7L1 | NR_134563.3 | n.642T>G | non_coding_transcript_exon_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPL7L1 | ENST00000493763.7 | c.453T>G | p.Phe151Leu | missense_variant | 5/6 | 1 | NM_001366481.3 | ENSP00000418221.3 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152132Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251324Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135858
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GnomAD4 exome AF: 0.0000105 AC: 15AN: 1433272Hom.: 0 Cov.: 26 AF XY: 0.00000699 AC XY: 5AN XY: 714964
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GnomAD4 genome AF: 0.000151 AC: 23AN: 152132Hom.: 0 Cov.: 31 AF XY: 0.000161 AC XY: 12AN XY: 74316
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | The c.426T>G (p.F142L) alteration is located in exon 5 (coding exon 5) of the RPL7L1 gene. This alteration results from a T to G substitution at nucleotide position 426, causing the phenylalanine (F) at amino acid position 142 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
.;T
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
PrimateAI
Uncertain
T
REVEL
Benign
MVP
MPC
ClinPred
T
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at