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GeneBe

19-49490270-A-G

Variant summary

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

The NM_012423.4(RPL13A):c.127A>G(p.Ile43Val) 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)
Exomes 𝑓: 0.0000040 ( 0 hom. )

Consequence

RPL13A
NM_012423.4 missense

Scores

2
7
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 8.53

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.127A>G p.Ile43Val missense_variant 3/8 ENST00000391857.9
RPL13ANM_001270491.2 linkuse as main transcriptc.-29-205A>G intron_variant
RPL13ANR_073024.2 linkuse as main transcriptn.139A>G non_coding_transcript_exon_variant 3/8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPL13AENST00000391857.9 linkuse as main transcriptc.127A>G p.Ile43Val missense_variant 3/81 NM_012423.4 P1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251414
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135890
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000958
AC:
14
AN:
1461882
Hom.:
0
AF XY:
0.0000138
AC XY:
10
AN XY:
727242
show subpopulations
Gnomad4 AFR exome
AF:
0.000179
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000497
Bravo
AF:
0.00000756

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 GeneticsAug 09, 2021The c.127A>G (p.I43V) alteration is located in exon 3 (coding exon 3) of the RPL13A gene. This alteration results from a A to G substitution at nucleotide position 127, causing the isoleucine (I) at amino acid position 43 to be replaced by a valine (V). 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
Uncertain
0.45
BayesDel_addAF
Uncertain
0.015
T
BayesDel_noAF
Benign
-0.12
Cadd
Uncertain
24
Dann
Uncertain
1.0
DEOGEN2
Benign
0.22
T
Eigen
Uncertain
0.34
Eigen_PC
Uncertain
0.43
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Pathogenic
0.97
D
M_CAP
Benign
0.015
T
MetaRNN
Uncertain
0.49
T
MetaSVM
Benign
-0.77
T
MutationAssessor
Benign
0.83
L
MutationTaster
Benign
1.0
D
PROVEAN
Benign
-0.87
N
REVEL
Uncertain
0.34
Sift
Benign
0.052
T
Sift4G
Benign
0.094
T
Polyphen
0.52
P
Vest4
0.61
MutPred
0.63
Gain of MoRF binding (P = 0.1025);
MVP
0.53
MPC
0.85
ClinPred
0.63
D
GERP RS
4.9
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.21
gMVP
0.67

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1279600358; hg19: chr19-49993527; API