Genetic Variant NM_023018.5:c.1334_1336delAGG (chr1-1752908-CCCT-C) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP3BA1

The NM_023018.5(NADK):c.1334_1336delAGG(p.Glu445del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00645 in 1,467,238 control chromosomes in the GnomAD database, including 135 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.020 ( 76 hom., cov: 0)

Exomes 𝑓: 0.0049 ( 59 hom. )

Consequence

NADK
NM_023018.5 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.426

Publications

4 publications found

Variant links:

Genes affected

NADK (HGNC:29831): (NAD kinase) NADK catalyzes the transfer of a phosphate group from ATP to NAD to generate NADP, which in its reduced form acts as an electron donor for biosynthetic reactions (Lerner et al., 2001 [PubMed 11594753]).[supplied by OMIM, Mar 2008]

NADK links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -9 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_023018.5

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NADK	NM_023018.5 link	c.1334_1336delAGG	p.Glu445del	disruptive_inframe_deletion	Exon 12 of 12	ENST00000341426.9	NP_075394.3	O95544-1A0A024R058

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NADK	ENST00000341426.9 link	c.1334_1336delAGG	p.Glu445del	disruptive_inframe_deletion	Exon 12 of 12	2	NM_023018.5	ENSP00000341679.5		O95544-1

Frequencies

GnomAD3 genomes

AF:

0.0201

AC:

3013

AN:

149788

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0594

Gnomad AMI

AF:

0.00111

Gnomad AMR

AF:

0.0189

Gnomad ASJ

AF:

0.00116

Gnomad EAS

AF:

0.00139

Gnomad SAS

AF:

0.000851

Gnomad FIN

AF:

0.0136

Gnomad MID

AF:

0.00955

Gnomad NFE

AF:

0.00156

Gnomad OTH

AF:

0.0171

GnomAD2 exomes

AF:

0.0148

AC:

2411

AN:

162868

AF XY:

0.0136

show subpopulations

Gnomad AFR exome

AF:

0.0708

Gnomad AMR exome

AF:

0.0140

Gnomad ASJ exome

AF:

0.0116

Gnomad EAS exome

AF:

0.00646

Gnomad FIN exome

AF:

0.0163

Gnomad NFE exome

AF:

0.00837

Gnomad OTH exome

AF:

0.0137

GnomAD4 exome

AF:

0.00486

AC:

6407

AN:

1317340

Hom.:

AF XY:

0.00473

AC XY:

3077

AN XY:

650634

show subpopulations

African (AFR)

AF:

0.0719

AC:

2141

AN:

29798

American (AMR)

AF:

0.0123

AC:

432

AN:

35248

Ashkenazi Jewish (ASJ)

AF:

0.00560

AC:

129

AN:

23024

East Asian (EAS)

AF:

0.00309

AC:

106

AN:

34352

South Asian (SAS)

AF:

0.00624

AC:

451

AN:

72230

European-Finnish (FIN)

AF:

0.0115

AC:

537

AN:

46496

Middle Eastern (MID)

AF:

0.00864

AC:

AN:

5322

European-Non Finnish (NFE)

AF:

0.00210

AC:

2136

AN:

1016616

Other (OTH)

AF:

0.00791

AC:

429

AN:

54254

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.427

Heterozygous variant carriers

260

519

779

1038

1298

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0204

AC:

3061

AN:

149898

Hom.:

Cov.:

AF XY:

0.0203

AC XY:

1487

AN XY:

73072

show subpopulations

African (AFR)

AF:

0.0604

AC:

2480

AN:

41028

American (AMR)

AF:

0.0189

AC:

284

AN:

15022

Ashkenazi Jewish (ASJ)

AF:

0.00116

AC:

AN:

3454

East Asian (EAS)

AF:

0.00139

AC:

AN:

5030

South Asian (SAS)

AF:

0.000853

AC:

AN:

4692

European-Finnish (FIN)

AF:

0.0136

AC:

139

AN:

10204

Middle Eastern (MID)

AF:

0.00685

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00156

AC:

105

AN:

67212

Other (OTH)

AF:

0.0170

AC:

AN:

2062

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

135

269

404

538

673

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0232

Hom.:

868

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.43

Mutation Taster

=76/24

polymorphism

(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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NM_023018.5:c.1334_1336delAGG

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