Variant rs561 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_005001.5(NDUFA7):c.300C>T(p.Pro100=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 1,611,872 control chromosomes in the GnomAD database, including 27,727 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.16 ( 2232 hom., cov: 32)

Exomes 𝑓: 0.18 ( 25495 hom. )

Consequence

NDUFA7
NM_005001.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.33

Variant links:

Genes affected

NDUFA7 (HGNC:7691): (NADH:ubiquinone oxidoreductase subunit A7) This gene encodes a subunit of NADH:ubiquinone oxidoreductase (complex I), which is a multiprotein complex located in the inner mitochondrial membrane. Complex I functions in the transfer of electrons from NADH to the respiratory chain. [provided by RefSeq, Mar 2011]

NDUFA7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP7

Synonymous conserved (PhyloP=-1.33 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NDUFA7	NM_005001.5 linkuse as main transcript	c.300C>T	p.Pro100=	synonymous_variant	4/4	ENST00000301457.3	NP_004992.2
NDUFA7	NR_135539.2 linkuse as main transcript	n.317C>T		non_coding_transcript_exon_variant	4/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NDUFA7	ENST00000301457.3 linkuse as main transcript	c.300C>T	p.Pro100=	synonymous_variant	4/4	1	NM_005001.5	ENSP00000301457	P1

Frequencies

GnomAD3 genomes

AF:

0.156

AC:

23679

AN:

152066

Hom.:

2233

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0511

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.258

Gnomad ASJ

AF:

0.196

Gnomad EAS

AF:

0.218

Gnomad SAS

AF:

0.0758

Gnomad FIN

AF:

0.183

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.189

Gnomad OTH

AF:

0.195

GnomAD3 exomes

AF:

0.181

AC:

44832

AN:

247198

Hom.:

4863

AF XY:

0.173

AC XY:

23170

AN XY:

134276

show subpopulations

Gnomad AFR exome

AF:

0.0433

Gnomad AMR exome

AF:

0.301

Gnomad ASJ exome

AF:

0.191

Gnomad EAS exome

AF:

0.214

Gnomad SAS exome

AF:

0.0655

Gnomad FIN exome

AF:

0.190

Gnomad NFE exome

AF:

0.187

Gnomad OTH exome

AF:

0.199

GnomAD4 exome

AF:

0.181

AC:

264190

AN:

1459688

Hom.:

25495

Cov.:

AF XY:

0.177

AC XY:

128717

AN XY:

726098

show subpopulations

Gnomad4 AFR exome

AF:

0.0428

Gnomad4 AMR exome

AF:

0.291

Gnomad4 ASJ exome

AF:

0.186

Gnomad4 EAS exome

AF:

0.198

Gnomad4 SAS exome

AF:

0.0671

Gnomad4 FIN exome

AF:

0.190

Gnomad4 NFE exome

AF:

0.188

Gnomad4 OTH exome

AF:

0.180

GnomAD4 genome

AF:

0.156

AC:

23676

AN:

152184

Hom.:

2232

Cov.:

AF XY:

0.155

AC XY:

11566

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.0510

Gnomad4 AMR

AF:

0.257

Gnomad4 ASJ

AF:

0.196

Gnomad4 EAS

AF:

0.219

Gnomad4 SAS

AF:

0.0750

Gnomad4 FIN

AF:

0.183

Gnomad4 NFE

AF:

0.189

Gnomad4 OTH

AF:

0.193

Alfa

AF:

0.178

Hom.:

5709

Bravo

AF:

0.158

Asia WGS

AF:

0.155

AC:

542

AN:

3478

EpiCase

AF:

0.180

EpiControl

AF:

0.188

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

5.7

DANN

Benign

0.84

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

Other links and lift over