Variant rs4147672 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005002.5(NDUFA9):c.318+49G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 1,473,734 control chromosomes in the GnomAD database, including 51,859 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.27 ( 5770 hom., cov: 32)

Exomes 𝑓: 0.26 ( 46089 hom. )

Consequence

NDUFA9
NM_005002.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.143

Variant links:

Genes affected

NDUFA9 (HGNC:7693): (NADH:ubiquinone oxidoreductase subunit A9) The encoded protein is a subunit of the hydrophobic protein fraction of the NADH:ubiquinone oxidoreductase (complex I), the first enzyme complex in the electron transport chain located in the inner mitochondrial membrane. A pseudogene has been identified on chromosome 12. [provided by RefSeq, May 2010]

NDUFA9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 12-4654971-G-A is Benign according to our data. Variant chr12-4654971-G-A is described in ClinVar as [Benign]. Clinvar id is 1243518.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NDUFA9	NM_005002.5 linkuse as main transcript	c.318+49G>A		intron_variant		ENST00000266544.10	NP_004993.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NDUFA9	ENST00000266544.10 linkuse as main transcript	c.318+49G>A		intron_variant		1	NM_005002.5	ENSP00000266544	P1

Frequencies

GnomAD3 genomes

AF:

0.272

AC:

41325

AN:

151784

Hom.:

5774

Cov.:

show subpopulations

Gnomad AFR

AF:

0.291

Gnomad AMI

AF:

0.291

Gnomad AMR

AF:

0.257

Gnomad ASJ

AF:

0.367

Gnomad EAS

AF:

0.191

Gnomad SAS

AF:

0.171

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.282

Gnomad OTH

AF:

0.310

GnomAD3 exomes

AF:

0.251

AC:

59025

AN:

235540

Hom.:

7658

AF XY:

0.250

AC XY:

31771

AN XY:

127238

show subpopulations

Gnomad AFR exome

AF:

0.293

Gnomad AMR exome

AF:

0.220

Gnomad ASJ exome

AF:

0.369

Gnomad EAS exome

AF:

0.189

Gnomad SAS exome

AF:

0.169

Gnomad FIN exome

AF:

0.198

Gnomad NFE exome

AF:

0.283

Gnomad OTH exome

AF:

0.274

GnomAD4 exome

AF:

0.260

AC:

343040

AN:

1321832

Hom.:

46089

Cov.:

AF XY:

0.259

AC XY:

171894

AN XY:

663994

show subpopulations

Gnomad4 AFR exome

AF:

0.293

Gnomad4 AMR exome

AF:

0.222

Gnomad4 ASJ exome

AF:

0.367

Gnomad4 EAS exome

AF:

0.155

Gnomad4 SAS exome

AF:

0.170

Gnomad4 FIN exome

AF:

0.201

Gnomad4 NFE exome

AF:

0.271

Gnomad4 OTH exome

AF:

0.269

GnomAD4 genome

AF:

0.272

AC:

41343

AN:

151902

Hom.:

5770

Cov.:

AF XY:

0.264

AC XY:

19634

AN XY:

74238

show subpopulations

Gnomad4 AFR

AF:

0.291

Gnomad4 AMR

AF:

0.257

Gnomad4 ASJ

AF:

0.367

Gnomad4 EAS

AF:

0.191

Gnomad4 SAS

AF:

0.172

Gnomad4 FIN

AF:

0.198

Gnomad4 NFE

AF:

0.282

Gnomad4 OTH

AF:

0.308

Alfa

AF:

0.285

Hom.:

13200

Bravo

AF:

0.277

Asia WGS

AF:

0.217

AC:

758

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 23, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.6

DANN

Benign

0.35

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