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GeneBe

19-49491055-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PM2_Supporting

The NM_012423.4(RPL13A):c.358G>C(p.Val120Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

RPL13A
NM_012423.4 missense

Scores

3
6
6

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.46

Links

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 33.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPL13ANM_012423.4 linkuse as main transcriptc.358G>C p.Val120Leu missense_variant 6/8 ENST00000391857.9
RPL13ANM_001270491.2 linkuse as main transcriptc.175G>C p.Val59Leu missense_variant 5/7
RPL13ANR_073024.2 linkuse as main transcriptn.370G>C non_coding_transcript_exon_variant 6/8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPL13AENST00000391857.9 linkuse as main transcriptc.358G>C p.Val120Leu missense_variant 6/81 NM_012423.4 P1

Frequencies

GnomAD3 genomes
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJul 19, 2022The c.358G>C (p.V120L) alteration is located in exon 6 (coding exon 6) of the RPL13A gene. This alteration results from a G to C substitution at nucleotide position 358, causing the valine (V) at amino acid position 120 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.92
BayesDel_addAF
Pathogenic
0.24
D
BayesDel_noAF
Uncertain
0.11
Cadd
Uncertain
25
Dann
Uncertain
1.0
DEOGEN2
Benign
0.13
T;D
Eigen
Uncertain
0.33
Eigen_PC
Uncertain
0.49
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Benign
0.84
T;T
M_CAP
Benign
0.0086
T
MetaRNN
Uncertain
0.62
D;D
MetaSVM
Benign
-0.61
T
MutationTaster
Benign
1.0
D
PrimateAI
Uncertain
0.79
T
Sift4G
Benign
0.070
T;T
Polyphen
0.0070
.;B
Vest4
0.76
MutPred
0.52
.;Loss of methylation at K115 (P = 0.0718);
MVP
0.66
MPC
0.47
ClinPred
0.96
D
GERP RS
5.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.43
gMVP
0.77

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-49994312; API