chr16-89562344-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_000977.4(RPL13):āc.430C>Gā(p.Leu144Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,188 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_000977.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPL13 | NM_000977.4 | c.430C>G | p.Leu144Val | missense_variant | 5/6 | ENST00000311528.10 | |
RPL13 | NM_033251.2 | c.430C>G | p.Leu144Val | missense_variant | 4/5 | ||
RPL13 | NM_001243131.1 | c.289C>G | p.Leu97Val | missense_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPL13 | ENST00000311528.10 | c.430C>G | p.Leu144Val | missense_variant | 5/6 | 1 | NM_000977.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152220Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1460968Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726812
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74362
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.430C>G (p.L144V) alteration is located in exon 1 (coding exon 1) of the RPL13 gene. This alteration results from a C to G substitution at nucleotide position 430, causing the leucine (L) at amino acid position 144 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at