dbSNP rs2288414: NDUFA7:c.101+89G>C (chr19-8320768-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005001.5(NDUFA7):c.101+89G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0536 in 1,502,462 control chromosomes in the GnomAD database, including 6,006 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 0.13 ( 2798 hom., cov: 32)

Exomes 𝑓: 0.045 ( 3208 hom. )

Consequence

NDUFA7
NM_005001.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.449

Publications

6 publications found

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:

ENSG00000167774 (HGNC:):

ENSG00000167774 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDUFA7	NM_005001.5 link	c.101+89G>C		intron_variant	Intron 2 of 3	ENST00000301457.3	NP_004992.2
NDUFA7	NR_135539.2 link	n.118+89G>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NDUFA7	ENST00000301457.3 link	c.101+89G>C		intron_variant	Intron 2 of 3	1	NM_005001.5	ENSP00000301457.1
ENSG00000167774	ENST00000598884.1 link	n.101+89G>C		intron_variant	Intron 2 of 4	4		ENSP00000470609.1

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19760

AN:

152042

Hom.:

2780

Cov.:

show subpopulations

Gnomad AFR

AF:

0.359

Gnomad AMI

AF:

0.0231

Gnomad AMR

AF:

0.0717

Gnomad ASJ

AF:

0.0579

Gnomad EAS

AF:

0.0888

Gnomad SAS

AF:

0.0393

Gnomad FIN

AF:

0.0297

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0348

Gnomad OTH

AF:

0.112

GnomAD4 exome

AF:

0.0449

AC:

60688

AN:

1350302

Hom.:

3208

AF XY:

0.0436

AC XY:

29429

AN XY:

674820

show subpopulations

African (AFR)

AF:

0.368

AC:

11364

AN:

30888

American (AMR)

AF:

0.0501

AC:

2186

AN:

43638

Ashkenazi Jewish (ASJ)

AF:

0.0605

AC:

1493

AN:

24660

East Asian (EAS)

AF:

0.0728

AC:

2825

AN:

38812

South Asian (SAS)

AF:

0.0346

AC:

2859

AN:

82730

European-Finnish (FIN)

AF:

0.0282

AC:

1468

AN:

52058

Middle Eastern (MID)

AF:

0.0672

AC:

370

AN:

5510

European-Non Finnish (NFE)

AF:

0.0341

AC:

34628

AN:

1015570

Other (OTH)

AF:

0.0619

AC:

3495

AN:

56436

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

2727

5454

8180

10907

13634

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1496

2992

4488

5984

7480

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.130

AC:

19816

AN:

152160

Hom.:

2798

Cov.:

AF XY:

0.129

AC XY:

9597

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.360

AC:

14915

AN:

41478

American (AMR)

AF:

0.0716

AC:

1093

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.0579

AC:

201

AN:

3472

East Asian (EAS)

AF:

0.0890

AC:

461

AN:

5178

South Asian (SAS)

AF:

0.0391

AC:

189

AN:

4828

European-Finnish (FIN)

AF:

0.0297

AC:

315

AN:

10612

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0348

AC:

2369

AN:

68016

Other (OTH)

AF:

0.110

AC:

232

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

748

1496

2245

2993

3741

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

368

552

736

920

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0850

Hom.:

185

Bravo

AF:

0.144

Asia WGS

AF:

0.0860

AC:

301

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.0

(source)

DANN

Benign

0.50

PhyloP100

-0.45

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over