Variant 21-42903480-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_021075.4(NDUFV3):c.468T>G(p.Ser156=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 1,613,890 control chromosomes in the GnomAD database, including 294,435 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.61 ( 28603 hom., cov: 32)

Exomes 𝑓: 0.60 ( 265832 hom. )

Consequence

NDUFV3
NM_021075.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.25

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 21-42903480-T-G is Benign according to our data. Variant chr21-42903480-T-G is described in ClinVar as [Benign]. Clinvar id is 1290051.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.25 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
NDUFV3	NM_021075.4 linkuse as main transcript	c.468T>G	p.Ser156=	synonymous_variant	3/4	ENST00000354250.7
NDUFV3	XM_011529586.3 linkuse as main transcript	c.468T>G	p.Ser156=	synonymous_variant	3/5
NDUFV3	NM_001001503.2 linkuse as main transcript	c.170-5384T>G		intron_variant
NDUFV3	XM_017028359.2 linkuse as main transcript	c.170-3360T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NDUFV3	ENST00000354250.7 linkuse as main transcript	c.468T>G	p.Ser156=	synonymous_variant	3/4	1	NM_021075.4		P56181-2
NDUFV3	ENST00000340344.4 linkuse as main transcript	c.170-5384T>G		intron_variant		1		P1	P56181-1
NDUFV3	ENST00000460259.1 linkuse as main transcript	n.991T>G		non_coding_transcript_exon_variant	5/6	2
NDUFV3	ENST00000460740.1 linkuse as main transcript	n.360T>G		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.605

AC:

91900

AN:

151918

Hom.:

28560

Cov.:

show subpopulations

Gnomad AFR

AF:

0.713

Gnomad AMI

AF:

0.603

Gnomad AMR

AF:

0.429

Gnomad ASJ

AF:

0.573

Gnomad EAS

AF:

0.339

Gnomad SAS

AF:

0.560

Gnomad FIN

AF:

0.629

Gnomad MID

AF:

0.618

Gnomad NFE

AF:

0.602

Gnomad OTH

AF:

0.557

GnomAD3 exomes

AF:

0.551

AC:

138534

AN:

251430

Hom.:

40186

AF XY:

0.557

AC XY:

75681

AN XY:

135898

show subpopulations

Gnomad AFR exome

AF:

0.720

Gnomad AMR exome

AF:

0.335

Gnomad ASJ exome

AF:

0.578

Gnomad EAS exome

AF:

0.329

Gnomad SAS exome

AF:

0.567

Gnomad FIN exome

AF:

0.628

Gnomad NFE exome

AF:

0.608

Gnomad OTH exome

AF:

0.541

GnomAD4 exome

AF:

0.599

AC:

875170

AN:

1461854

Hom.:

265832

Cov.:

AF XY:

0.598

AC XY:

435071

AN XY:

727226

show subpopulations

Gnomad4 AFR exome

AF:

0.718

Gnomad4 AMR exome

AF:

0.345

Gnomad4 ASJ exome

AF:

0.570

Gnomad4 EAS exome

AF:

0.366

Gnomad4 SAS exome

AF:

0.573

Gnomad4 FIN exome

AF:

0.627

Gnomad4 NFE exome

AF:

0.616

Gnomad4 OTH exome

AF:

0.575

GnomAD4 genome

AF:

0.605

AC:

91991

AN:

152036

Hom.:

28603

Cov.:

AF XY:

0.602

AC XY:

44732

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.713

Gnomad4 AMR

AF:

0.428

Gnomad4 ASJ

AF:

0.573

Gnomad4 EAS

AF:

0.339

Gnomad4 SAS

AF:

0.560

Gnomad4 FIN

AF:

0.629

Gnomad4 NFE

AF:

0.602

Gnomad4 OTH

AF:

0.561

Alfa

AF:

0.588

Hom.:

41226

Bravo

AF:

0.591

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.058

DANN

Benign

0.44

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over