10-100526413-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1PM2BP4_Strong

The NM_005004.4(NDUFB8):ā€‹c.454G>Cā€‹(p.Val152Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000207 in 1,447,854 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.0000021 ( 0 hom. )

Consequence

NDUFB8
NM_005004.4 missense

Scores

19

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.796
Variant links:
Genes affected
NDUFB8 (HGNC:7703): (NADH:ubiquinone oxidoreductase subunit B8) Involved in mitochondrial respiratory chain complex I assembly. Located in endoplasmic reticulum and mitochondrion. Part of mitochondrial respiratory chain complex I. Implicated in nuclear type mitochondrial complex I deficiency 32. Biomarker of Alzheimer's disease and Parkinson's disease. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM1
In a chain NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial (size 157) in uniprot entity NDUB8_HUMAN there are 5 pathogenic changes around while only 0 benign (100%) in NM_005004.4
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.04824379).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NDUFB8NM_005004.4 linkc.454G>C p.Val152Leu missense_variant Exon 4 of 5 ENST00000299166.9 NP_004995.1 O95169-1
NDUFB8NM_001284367.2 linkc.454G>C p.Val152Leu missense_variant Exon 4 of 5 NP_001271296.1 O95169-2
NDUFB8NM_001284368.1 linkc.361G>C p.Val121Leu missense_variant Exon 4 of 5 NP_001271297.1 O95169-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NDUFB8ENST00000299166.9 linkc.454G>C p.Val152Leu missense_variant Exon 4 of 5 1 NM_005004.4 ENSP00000299166.4 O95169-1
ENSG00000255339ENST00000557395.5 linkn.454G>C non_coding_transcript_exon_variant Exon 4 of 10 2 ENSP00000456832.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000420
AC:
1
AN:
238054
Hom.:
0
AF XY:
0.00000774
AC XY:
1
AN XY:
129260
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
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:
0.00000910
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000207
AC:
3
AN:
1447854
Hom.:
0
Cov.:
30
AF XY:
0.00000278
AC XY:
2
AN XY:
720488
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:
0.00000271
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000756
ExAC
AF:
0.00000824
AC:
1

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Uncertain:1
Sep 01, 2021
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant is present in population databases (rs763076321, ExAC 0.002%). This variant has not been reported in the literature in individuals affected with NDUFB8-related conditions. This sequence change replaces valine with leucine at codon 152 of the NDUFB8 protein (p.Val152Leu). The valine residue is weakly conserved and there is a small physicochemical difference between valine and leucine. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.23
BayesDel_addAF
Benign
-0.32
T
BayesDel_noAF
Benign
-0.70
CADD
Benign
0.0080
DANN
Benign
0.54
DEOGEN2
Benign
0.025
T;.;.
Eigen
Benign
-2.3
Eigen_PC
Benign
-2.4
FATHMM_MKL
Benign
0.20
N
LIST_S2
Benign
0.84
T;T;.
M_CAP
Benign
0.0023
T
MetaRNN
Benign
0.048
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.2
L;.;L
PrimateAI
Benign
0.27
T
PROVEAN
Benign
0.060
N;N;N
REVEL
Benign
0.032
Sift
Benign
0.65
T;T;T
Sift4G
Benign
0.70
T;T;T
Polyphen
0.0030
B;.;.
Vest4
0.057
MutPred
0.28
Loss of catalytic residue at Q154 (P = 0.1122);.;Loss of catalytic residue at Q154 (P = 0.1122);
MVP
0.081
MPC
0.24
ClinPred
0.035
T
GERP RS
-11
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.26
gMVP
0.74

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: rs763076321; hg19: chr10-102286170; API