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GeneBe

19-49491452-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.430G>C(p.Glu144Gln) 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: 29)

Consequence

RPL13A
NM_012423.4 missense

Scores

6
4
5

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 9.63

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 29.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPL13ANM_012423.4 linkuse as main transcriptc.430G>C p.Glu144Gln missense_variant 7/8 ENST00000391857.9
RPL13ANM_001270491.2 linkuse as main transcriptc.247G>C p.Glu83Gln missense_variant 6/7
RPL13ANR_073024.2 linkuse as main transcriptn.442G>C non_coding_transcript_exon_variant 7/8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPL13AENST00000391857.9 linkuse as main transcriptc.430G>C p.Glu144Gln missense_variant 7/81 NM_012423.4 P1

Frequencies

GnomAD3 genomes
Cov.:
29
GnomAD4 exome
AF:
8.72e-7
AC:
1
AN:
1146834
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
567212
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000114
Gnomad4 OTH exome
AF:
0.00

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 GeneticsApr 12, 2023The c.430G>C (p.E144Q) alteration is located in exon 7 (coding exon 7) of the RPL13A gene. This alteration results from a G to C substitution at nucleotide position 430, causing the glutamic acid (E) at amino acid position 144 to be replaced by a glutamine (Q). 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
0.96
BayesDel_addAF
Pathogenic
0.30
D
BayesDel_noAF
Pathogenic
0.19
Cadd
Uncertain
25
Dann
Uncertain
1.0
DEOGEN2
Benign
0.12
T;D
Eigen
Pathogenic
0.78
Eigen_PC
Pathogenic
0.77
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Benign
0.84
T;T
M_CAP
Benign
0.043
D
MetaRNN
Uncertain
0.71
D;D
MetaSVM
Uncertain
-0.20
T
MutationTaster
Benign
1.0
D
PrimateAI
Uncertain
0.79
T
Sift4G
Benign
0.11
T;T
Polyphen
0.97
.;D
Vest4
0.77
MutPred
0.40
.;Gain of MoRF binding (P = 0.062);
MVP
0.71
MPC
1.0
ClinPred
0.99
D
GERP RS
5.7
Varity_R
0.36
gMVP
0.80

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.11
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: chr19-49994709; API