rs10057103

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001331026.2(NNT):​c.-118C>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)

Consequence

NNT
NM_001331026.2 5_prime_UTR_premature_start_codon_gain

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.126
Variant links:
Genes affected
NNT (HGNC:7863): (nicotinamide nucleotide transhydrogenase) This gene encodes an integral protein of the inner mitochondrial membrane. The enzyme couples hydride transfer between NAD(H) and NADP(+) to proton translocation across the inner mitochondrial membrane. Under most physiological conditions, the enzyme uses energy from the mitochondrial proton gradient to produce high concentrations of NADPH. The resulting NADPH is used for biosynthesis and in free radical detoxification. [provided by RefSeq, Sep 2016]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.055696905).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NNTNM_182977.3 linkc.46C>G p.Leu16Val missense_variant Exon 2 of 22 ENST00000344920.9 NP_892022.2 Q13423A0A024R0C3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NNTENST00000344920.9 linkc.46C>G p.Leu16Val missense_variant Exon 2 of 22 1 NM_182977.3 ENSP00000343873.4 Q13423

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
38
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.056
BayesDel_addAF
Uncertain
0.019
T
BayesDel_noAF
Benign
-0.21
CADD
Benign
13
DANN
Benign
0.94
DEOGEN2
Benign
0.0074
.;T;T;T
Eigen
Benign
-0.81
Eigen_PC
Benign
-0.61
FATHMM_MKL
Benign
0.50
D
LIST_S2
Benign
0.60
T;T;.;T
M_CAP
Benign
0.048
D
MetaRNN
Benign
0.056
T;T;T;T
MetaSVM
Uncertain
-0.19
T
MutationAssessor
Benign
0.14
.;.;N;N
PrimateAI
Benign
0.26
T
PROVEAN
Benign
-0.010
N;N;N;N
REVEL
Benign
0.29
Sift
Benign
0.51
T;T;T;T
Sift4G
Benign
0.13
T;T;T;T
Polyphen
0.0
.;.;B;B
Vest4
0.11
MutPred
0.20
Loss of helix (P = 0.1299);Loss of helix (P = 0.1299);Loss of helix (P = 0.1299);Loss of helix (P = 0.1299);
MVP
0.44
MPC
0.26
ClinPred
0.052
T
GERP RS
3.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.6
Varity_R
0.034
gMVP
0.42

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: rs10057103; hg19: chr5-43609343; API