Variant chr2-37231668-CA-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_144736.5(NDUFAF7):c.-37delA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0294 in 1,614,176 control chromosomes in the GnomAD database, including 817 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.022 ( 48 hom., cov: 32)

Exomes 𝑓: 0.030 ( 769 hom. )

Consequence

NDUFAF7
NM_144736.5 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.22

Variant links:

Genes affected

NDUFAF7 (HGNC:28816): (NADH:ubiquinone oxidoreductase complex assembly factor 7) This gene encodes an assembly factor protein which helps in the assembly and stabilization of Complex I, a large multi-subunit enzyme in the mitochondrial respiratory chain. Complex I is involved in several physiological activities in the cell, including metabolite transport and ATP synthesis. The encoded protein is a methyltransferase which methylates Arg85 of a subunit of Complex I in the early stages of its assembly. A pseudogene related to this gene is located on chromosome 8. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

NDUFAF7 links:

NDUFAF7 (HGNC:):

NDUFAF7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 2-37231668-CA-C is Benign according to our data. Variant chr2-37231668-CA-C is described in ClinVar as [Benign]. Clinvar id is 214756.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0216 (3286/152336) while in subpopulation SAS AF= 0.04 (193/4830). AF 95% confidence interval is 0.0353. There are 48 homozygotes in gnomad4. There are 1643 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 48 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NDUFAF7	NM_144736.5 linkuse as main transcript	c.-37delA		5_prime_UTR_variant	1/10	ENST00000002125.9	NP_653337.1	Q7L592-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NDUFAF7	ENST00000002125 linkuse as main transcript	c.-37delA		5_prime_UTR_variant	1/10	1	NM_144736.5	ENSP00000002125.4		Q7L592-1

Frequencies

GnomAD3 genomes

AF:

0.0216

AC:

3282

AN:

152218

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00601

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.0198

Gnomad ASJ

AF:

0.0324

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0393

Gnomad FIN

AF:

0.0245

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0306

Gnomad OTH

AF:

0.0335

GnomAD3 exomes

AF:

0.0255

AC:

6404

AN:

251140

Hom.:

125

AF XY:

0.0266

AC XY:

3610

AN XY:

135840

show subpopulations

Gnomad AFR exome

AF:

0.00567

Gnomad AMR exome

AF:

0.0154

Gnomad ASJ exome

AF:

0.0350

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.0344

Gnomad FIN exome

AF:

0.0268

Gnomad NFE exome

AF:

0.0317

Gnomad OTH exome

AF:

0.0316

GnomAD4 exome

AF:

0.0303

AC:

44248

AN:

1461840

Hom.:

769

Cov.:

AF XY:

0.0304

AC XY:

22096

AN XY:

727216

show subpopulations

Gnomad4 AFR exome

AF:

0.00636

Gnomad4 AMR exome

AF:

0.0167

Gnomad4 ASJ exome

AF:

0.0341

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0362

Gnomad4 FIN exome

AF:

0.0288

Gnomad4 NFE exome

AF:

0.0320

Gnomad4 OTH exome

AF:

0.0321

GnomAD4 genome

AF:

0.0216

AC:

3286

AN:

152336

Hom.:

Cov.:

AF XY:

0.0221

AC XY:

1643

AN XY:

74506

show subpopulations

Gnomad4 AFR

AF:

0.00601

Gnomad4 AMR

AF:

0.0198

Gnomad4 ASJ

AF:

0.0324

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0400

Gnomad4 FIN

AF:

0.0245

Gnomad4 NFE

AF:

0.0306

Gnomad4 OTH

AF:

0.0331

Alfa

AF:

0.0189

Hom.:

Bravo

AF:

0.0205

Asia WGS

AF:

0.0150

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 23, 2013

The variant is found in MITONUC-MITOP panel(s). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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