chr21-42903400-T-G

Variant summary

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

The NM_021075.4(NDUFV3):ā€‹c.388T>Gā€‹(p.Ser130Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,696 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 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‘“: 6.8e-7 ( 0 hom. )

Consequence

NDUFV3
NM_021075.4 missense

Scores

16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.856
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 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=0.06308186).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NDUFV3NM_021075.4 linkuse as main transcriptc.388T>G p.Ser130Ala missense_variant 3/4 ENST00000354250.7 NP_066553.3
NDUFV3XM_011529586.3 linkuse as main transcriptc.388T>G p.Ser130Ala missense_variant 3/5 XP_011527888.1
NDUFV3NM_001001503.2 linkuse as main transcriptc.170-5464T>G intron_variant NP_001001503.1
NDUFV3XM_017028359.2 linkuse as main transcriptc.170-3440T>G intron_variant XP_016883848.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NDUFV3ENST00000354250.7 linkuse as main transcriptc.388T>G p.Ser130Ala missense_variant 3/41 NM_021075.4 ENSP00000346196 P56181-2
NDUFV3ENST00000340344.4 linkuse as main transcriptc.170-5464T>G intron_variant 1 ENSP00000342895 P1P56181-1
NDUFV3ENST00000460259.1 linkuse as main transcriptn.911T>G non_coding_transcript_exon_variant 5/62
NDUFV3ENST00000460740.1 linkuse as main transcriptn.280T>G non_coding_transcript_exon_variant 2/22

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251492
Hom.:
0
AF XY:
0.00000736
AC XY:
1
AN XY:
135920
show subpopulations
Gnomad AFR exome
AF:
0.0000615
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:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461696
Hom.:
0
Cov.:
31
AF XY:
0.00000138
AC XY:
1
AN XY:
727164
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
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:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
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 specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsNov 30, 2022The c.388T>G (p.S130A) alteration is located in exon 3 (coding exon 3) of the NDUFV3 gene. This alteration results from a T to G substitution at nucleotide position 388, causing the serine (S) at amino acid position 130 to be replaced by an alanine (A). 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
BayesDel_addAF
Benign
-0.49
T
BayesDel_noAF
Benign
-0.75
CADD
Benign
0.62
DANN
Benign
0.67
Eigen
Benign
-1.1
Eigen_PC
Benign
-1.2
FATHMM_MKL
Benign
0.084
N
LIST_S2
Benign
0.47
T
M_CAP
Benign
0.015
T
MetaRNN
Benign
0.063
T
MetaSVM
Benign
-0.99
T
MutationTaster
Benign
1.0
N;N
PrimateAI
Benign
0.27
T
PROVEAN
Benign
-0.57
N
REVEL
Benign
0.057
Sift
Benign
0.57
T
Sift4G
Benign
0.80
T
Polyphen
0.28
B
Vest4
0.088
MutPred
0.14
Loss of phosphorylation at S130 (P = 0.0298);
MVP
0.48
MPC
0.088
ClinPred
0.057
T
GERP RS
-5.6
gMVP
0.085

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs11557449; hg19: chr21-44323510; API