1-151760163-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_031420.4(MRPL9):​c.691G>A​(p.Val231Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,840 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V231L) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000068 ( 0 hom. )

Consequence

MRPL9
NM_031420.4 missense

Scores

6
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.06
Variant links:
Genes affected
MRPL9 (HGNC:14277): (mitochondrial ribosomal protein L9) This is a nuclear gene encoding a protein component of the 39S subunit of the mitochondrial ribosome. Alternative splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 8. [provided by RefSeq, Jul 2014]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.19239342).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MRPL9NM_031420.4 linkc.691G>A p.Val231Met missense_variant Exon 7 of 7 ENST00000368830.8 NP_113608.1 Q9BYD2
MRPL9NM_001300733.2 linkc.589G>A p.Val197Met missense_variant Exon 6 of 6 NP_001287662.1 Q9BYD2Q5SZR1
MRPL9NR_125331.2 linkn.748G>A non_coding_transcript_exon_variant Exon 7 of 7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MRPL9ENST00000368830.8 linkc.691G>A p.Val231Met missense_variant Exon 7 of 7 1 NM_031420.4 ENSP00000357823.3 Q9BYD2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000684
AC:
10
AN:
1461840
Hom.:
0
Cov.:
30
AF XY:
0.00000825
AC XY:
6
AN XY:
727226
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:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000809
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.49
BayesDel_addAF
Benign
-0.047
T
BayesDel_noAF
Benign
-0.31
CADD
Benign
23
DANN
Benign
0.97
DEOGEN2
Benign
0.14
T;.
Eigen
Benign
-0.32
Eigen_PC
Benign
-0.29
FATHMM_MKL
Uncertain
0.88
D
LIST_S2
Uncertain
0.93
D;D
M_CAP
Benign
0.014
T
MetaRNN
Benign
0.19
T;T
MetaSVM
Benign
-0.97
T
MutationAssessor
Uncertain
2.3
M;.
PrimateAI
Benign
0.36
T
PROVEAN
Benign
-2.2
N;N
REVEL
Benign
0.19
Sift
Uncertain
0.0040
D;D
Sift4G
Uncertain
0.042
D;D
Polyphen
0.47
P;.
Vest4
0.36
MutPred
0.59
Loss of catalytic residue at V231 (P = 0.0062);.;
MVP
0.26
MPC
1.1
ClinPred
0.84
D
GERP RS
3.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.090
gMVP
0.79

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: chr1-151732639; API