Variant 2-37232065-C-T 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_144736.5(NDUFAF7):c.56-41C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0899 in 1,613,866 control chromosomes in the GnomAD database, including 10,788 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 1199 hom., cov: 33)

Exomes 𝑓: 0.089 ( 9589 hom. )

Consequence

NDUFAF7
NM_144736.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.521

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 2-37232065-C-T is Benign according to our data. Variant chr2-37232065-C-T is described in ClinVar as [Benign]. Clinvar id is 673729.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NDUFAF7	NM_144736.5 linkuse as main transcript	c.56-41C>T		intron_variant		ENST00000002125.9	NP_653337.1	Q7L592-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NDUFAF7	ENST00000002125.9 linkuse as main transcript	c.56-41C>T		intron_variant		1	NM_144736.5	ENSP00000002125.4		Q7L592-1

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15432

AN:

152112

Hom.:

1205

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0748

Gnomad AMI

AF:

0.0954

Gnomad AMR

AF:

0.223

Gnomad ASJ

AF:

0.0286

Gnomad EAS

AF:

0.362

Gnomad SAS

AF:

0.125

Gnomad FIN

AF:

0.134

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0677

Gnomad OTH

AF:

0.107

GnomAD3 exomes

AF:

0.141

AC:

35446

AN:

251068

Hom.:

4400

AF XY:

0.131

AC XY:

17737

AN XY:

135848

show subpopulations

Gnomad AFR exome

AF:

0.0736

Gnomad AMR exome

AF:

0.369

Gnomad ASJ exome

AF:

0.0317

Gnomad EAS exome

AF:

0.343

Gnomad SAS exome

AF:

0.119

Gnomad FIN exome

AF:

0.131

Gnomad NFE exome

AF:

0.0676

Gnomad OTH exome

AF:

0.112

GnomAD4 exome

AF:

0.0887

AC:

129703

AN:

1461636

Hom.:

9589

Cov.:

AF XY:

0.0880

AC XY:

64019

AN XY:

727118

show subpopulations

Gnomad4 AFR exome

AF:

0.0723

Gnomad4 AMR exome

AF:

0.346

Gnomad4 ASJ exome

AF:

0.0337

Gnomad4 EAS exome

AF:

0.356

Gnomad4 SAS exome

AF:

0.117

Gnomad4 FIN exome

AF:

0.129

Gnomad4 NFE exome

AF:

0.0664

Gnomad4 OTH exome

AF:

0.0943

GnomAD4 genome

AF:

0.101

AC:

15439

AN:

152230

Hom.:

1199

Cov.:

AF XY:

0.109

AC XY:

8076

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.0748

Gnomad4 AMR

AF:

0.223

Gnomad4 ASJ

AF:

0.0286

Gnomad4 EAS

AF:

0.362

Gnomad4 SAS

AF:

0.125

Gnomad4 FIN

AF:

0.134

Gnomad4 NFE

AF:

0.0677

Gnomad4 OTH

AF:

0.110

Alfa

AF:

0.0386

Hom.:

Bravo

AF:

0.111

Asia WGS

AF:

0.225

AC:

778

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 14, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.73

DANN

Benign

0.81

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