dbSNP rs77606940: NDUFV3:p.Pro4Gln (chr21-42893344-C-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_021075.4(NDUFV3):c.11C>A(p.Pro4Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000361 in 1,386,094 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000036 ( 0 hom. )

Consequence

NDUFV3
NM_021075.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.215

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]

NDUFV3 links:

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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=0.10628149).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDUFV3	NM_021075.4 link	c.11C>A	p.Pro4Gln	missense_variant	Exon 1 of 4	ENST00000354250.7	NP_066553.3	P56181-2
NDUFV3	NM_001001503.2 link	c.11C>A	p.Pro4Gln	missense_variant	Exon 1 of 3		NP_001001503.1	P56181-1
NDUFV3	XM_011529586.3 link	c.11C>A	p.Pro4Gln	missense_variant	Exon 1 of 5		XP_011527888.1
NDUFV3	XM_017028359.2 link	c.11C>A	p.Pro4Gln	missense_variant	Exon 1 of 4		XP_016883848.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
NDUFV3	ENST00000354250.7 link	c.11C>A	p.Pro4Gln	missense_variant	Exon 1 of 4	1	NM_021075.4	ENSP00000346196.2	P56181-2
NDUFV3	ENST00000340344.4 link	c.11C>A	p.Pro4Gln	missense_variant	Exon 1 of 3	1		ENSP00000342895.3	P56181-1
NDUFV3	ENST00000460740.1 link	n.24C>A		non_coding_transcript_exon_variant	Exon 1 of 2	2
NDUFV3	ENST00000460259.1 link	n.572-3583C>A		intron_variant	Intron 3 of 5	2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000361

AC:

AN:

1386094

Hom.:

Cov.:

AF XY:

0.00000146

AC XY:

AN XY:

684068

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:

0.0000126

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000371

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.096

BayesDel_addAF

Benign

-0.24

BayesDel_noAF

Benign

-0.59

CADD

Benign

0.93

DANN

Benign

0.64

DEOGEN2

Benign

0.0054

.;T

Eigen

Benign

-0.90

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.055

LIST_S2

Benign

0.44

T;T

M_CAP

Benign

0.0086

MetaRNN

Benign

0.11

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.69

N;N

PrimateAI

Benign

0.45

PROVEAN

Benign

-0.59

N;N

REVEL

Benign

0.025

Sift

Benign

0.31

T;D

Sift4G

Benign

0.13

T;T

Polyphen

0.74

P;P

Vest4

0.16

MutPred

0.27

Loss of catalytic residue at P4 (P = 0.0141);Loss of catalytic residue at P4 (P = 0.0141);

MVP

0.33

MPC

0.16

ClinPred

0.19

GERP RS

-0.21

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.034

gMVP

0.12

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

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