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GeneBe

19-49491432-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_012423.4(RPL13A):c.410A>G(p.Tyr137Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00018 ( 0 hom., cov: 19)
Exomes 𝑓: 0.000098 ( 0 hom. )

Consequence

RPL13A
NM_012423.4 missense

Scores

4
11

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.77

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
?
Computational evidence support a benign effect (MetaRNN=0.059810072).
BS2
?
High AC in GnomAd at 16 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPL13ANM_012423.4 linkuse as main transcriptc.410A>G p.Tyr137Cys missense_variant 7/8 ENST00000391857.9
RPL13ANM_001270491.2 linkuse as main transcriptc.227A>G p.Tyr76Cys missense_variant 6/7
RPL13ANR_073024.2 linkuse as main transcriptn.422A>G 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.410A>G p.Tyr137Cys missense_variant 7/81 NM_012423.4 P1

Frequencies

GnomAD3 genomes
AF:
0.000182
AC:
16
AN:
88144
Hom.:
0
Cov.:
19
show subpopulations
Gnomad AFR
AF:
0.000611
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000215
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000976
AC:
14
AN:
143392
Hom.:
0
AF XY:
0.000103
AC XY:
8
AN XY:
77954
show subpopulations
Gnomad AFR exome
AF:
0.000946
Gnomad AMR exome
AF:
0.000243
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000455
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000736
AC:
37
AN:
502888
Hom.:
0
AF XY:
0.0000620
AC XY:
16
AN XY:
257998
show subpopulations
Gnomad4 AFR exome
AF:
0.00167
Gnomad4 AMR exome
AF:
0.000255
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000159
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000177
Gnomad4 OTH exome
AF:
0.0000483
Alfa
AF:
0.000569
Hom.:
0
ExAC
AF:
0.0000544
AC:
6

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 GeneticsOct 12, 2022The c.410A>G (p.Y137C) alteration is located in exon 7 (coding exon 7) of the RPL13A gene. This alteration results from a A to G substitution at nucleotide position 410, causing the tyrosine (Y) at amino acid position 137 to be replaced by a cysteine (C). 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
Benign
0.11
BayesDel_addAF
Benign
-0.16
T
BayesDel_noAF
Uncertain
-0.070
Cadd
Benign
21
Dann
Uncertain
0.98
DEOGEN2
Benign
0.038
T;T
Eigen
Benign
-0.21
Eigen_PC
Benign
-0.016
FATHMM_MKL
Uncertain
0.90
D
LIST_S2
Benign
0.73
T;T
M_CAP
Benign
0.0083
T
MetaRNN
Benign
0.060
T;T
MetaSVM
Benign
-0.96
T
MutationTaster
Benign
0.61
D
PrimateAI
Uncertain
0.76
T
Sift4G
Benign
0.20
T;T
Polyphen
0.0010
.;B
Vest4
0.53
MutPred
0.38
.;Gain of relative solvent accessibility (P = 0.1259);
MVP
0.72
MPC
0.60
ClinPred
0.022
T
GERP RS
4.6
Varity_R
0.11
gMVP
0.80

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: rs764054618; hg19: chr19-49994689; API