chr21-42893356-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_021075.4(NDUFV3):​c.23G>T​(p.Arg8Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000488 in 1,538,210 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000053 ( 0 hom. )

Consequence

NDUFV3
NM_021075.4 missense

Scores

5
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.33
Variant links:
Genes affected
NDUFV3 (HGNC:7719): (NADH:ubiquinone oxidoreductase subunit V3) The protein encoded by this gene is one of at least forty-one subunits that make up the NADH-ubiquinone oxidoreductase complex. This complex is part of the mitochondrial respiratory chain and serves to catalyze the rotenone-sensitive oxidation of NADH and the reduction of ubiquinone. The encoded protein is one of three proteins found in the flavoprotein fraction of the complex. The specific function of the encoded protein is unknown. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3211668).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NDUFV3NM_021075.4 linkuse as main transcriptc.23G>T p.Arg8Leu missense_variant 1/4 ENST00000354250.7 NP_066553.3
NDUFV3NM_001001503.2 linkuse as main transcriptc.23G>T p.Arg8Leu missense_variant 1/3 NP_001001503.1
NDUFV3XM_011529586.3 linkuse as main transcriptc.23G>T p.Arg8Leu missense_variant 1/5 XP_011527888.1
NDUFV3XM_017028359.2 linkuse as main transcriptc.23G>T p.Arg8Leu missense_variant 1/4 XP_016883848.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NDUFV3ENST00000354250.7 linkuse as main transcriptc.23G>T p.Arg8Leu missense_variant 1/41 NM_021075.4 ENSP00000346196 P56181-2
NDUFV3ENST00000340344.4 linkuse as main transcriptc.23G>T p.Arg8Leu missense_variant 1/31 ENSP00000342895 P1P56181-1
NDUFV3ENST00000460740.1 linkuse as main transcriptn.36G>T non_coding_transcript_exon_variant 1/22
NDUFV3ENST00000460259.1 linkuse as main transcriptn.572-3571G>T intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152230
Hom.:
0
Cov.:
32
show subpopulations
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:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000149
AC:
2
AN:
134164
Hom.:
0
AF XY:
0.0000137
AC XY:
1
AN XY:
73106
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000409
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:
0.0000201
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000534
AC:
74
AN:
1385980
Hom.:
0
Cov.:
31
AF XY:
0.0000453
AC XY:
31
AN XY:
684002
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000280
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:
0.0000658
Gnomad4 OTH exome
AF:
0.0000347
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152230
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000434
Hom.:
0
Bravo
AF:
0.0000151

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsApr 11, 2023The c.23G>T (p.R8L) alteration is located in exon 1 (coding exon 1) of the NDUFV3 gene. This alteration results from a G to T substitution at nucleotide position 23, causing the arginine (R) at amino acid position 8 to be replaced by a leucine (L). 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
0.14
BayesDel_addAF
Benign
-0.072
T
BayesDel_noAF
Benign
-0.22
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.029
.;T
Eigen
Benign
-0.024
Eigen_PC
Benign
-0.12
FATHMM_MKL
Benign
0.73
D
LIST_S2
Benign
0.80
T;T
M_CAP
Benign
0.043
D
MetaRNN
Benign
0.32
T;T
MetaSVM
Benign
-0.96
T
MutationAssessor
Benign
1.8
L;L
MutationTaster
Benign
0.93
N;N
PrimateAI
Uncertain
0.61
T
PROVEAN
Uncertain
-4.3
D;N
REVEL
Benign
0.14
Sift
Uncertain
0.0030
D;D
Sift4G
Uncertain
0.0090
D;T
Polyphen
0.98
D;D
Vest4
0.47
MutPred
0.36
Loss of MoRF binding (P = 2e-04);Loss of MoRF binding (P = 2e-04);
MVP
0.39
MPC
0.36
ClinPred
0.94
D
GERP RS
2.4
RBP_binding_hub_radar
0.92
RBP_regulation_power_radar
3.0
Varity_R
0.12
gMVP
0.40

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: rs906856402; hg19: chr21-44313466; API