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GeneBe

11-1952192-G-A

Variant summary

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

The NM_021134.4(MRPL23):c.206G>A(p.Arg69Gln) variant causes a missense change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 1)
Exomes 𝑓: 0.000084 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

MRPL23
NM_021134.4 missense

Scores

9
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.71

Links

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MRPL23NM_021134.4 linkuse as main transcriptc.206G>A p.Arg69Gln missense_variant 3/5 ENST00000397298.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MRPL23ENST00000397298.8 linkuse as main transcriptc.206G>A p.Arg69Gln missense_variant 3/51 NM_021134.4 P1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
1
AN:
8048
Hom.:
0
Cov.:
1
FAILED QC
Gnomad AFR
AF:
0.00
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:
0.000171
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000837
AC:
21
AN:
250936
Hom.:
0
AF XY:
0.0000810
AC XY:
11
AN XY:
135808
show subpopulations
Gnomad AFR exome
AF:
0.0000618
Gnomad AMR exome
AF:
0.000347
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000706
Gnomad OTH exome
AF:
0.00
Alfa
AF:
0.0000761
Hom.:
0
ExAC
AF:
0.0000824
AC:
10
EpiCase
AF:
0.000109
EpiControl
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 GeneticsJul 26, 2021The c.206G>A (p.R69Q) alteration is located in exon 3 (coding exon 3) of the MRPL23 gene. This alteration results from a G to A substitution at nucleotide position 206, causing the arginine (R) at amino acid position 69 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
Uncertain
0.37
BayesDel_addAF
Benign
-0.15
T
BayesDel_noAF
Benign
-0.13
Cadd
Pathogenic
26
Dann
Uncertain
1.0
DEOGEN2
Benign
0.080
T;T;T;T;T
Eigen
Uncertain
0.31
Eigen_PC
Benign
0.12
FATHMM_MKL
Uncertain
0.94
D
M_CAP
Benign
0.044
D
MetaRNN
Uncertain
0.64
D;D;D;D;D
MetaSVM
Benign
-0.64
T
MutationAssessor
Uncertain
2.1
M;M;.;.;.
MutationTaster
Benign
1.0
D;D;D;D;D
PrimateAI
Uncertain
0.69
T
PROVEAN
Uncertain
-2.4
N;N;N;N;N
REVEL
Uncertain
0.38
Sift
Benign
0.049
D;D;D;D;D
Sift4G
Benign
0.065
T;T;D;D;D
Polyphen
1.0
D;D;.;.;.
Vest4
0.78
MVP
0.53
MPC
0.74
ClinPred
0.28
T
GERP RS
3.0
Varity_R
0.68
gMVP
0.59

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: rs753557034; hg19: chr11-1973422; COSMIC: COSV67414266; COSMIC: COSV67414266; API