1-1752908-CCCTCCTCCTCCTCCTCCT-CCCTCCTCCTCCT

Variant names:

• chr1-1752908-CCCTCCT-C
• rs71578334
• NM_023018.5:c.1331_1336delAGGAGG

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3

The NM_023018.5(NADK):​c.1331_1336delAGGAGG​(p.Glu444_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 0.000273 in 1,525,942 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00027 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00027 (0 hom.)
• Consequence: NADK NM_023018.5 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.426
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_023018.5

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NADK	NM_023018.5	c.1331_1336delAGGAGG	p.Glu444_Glu445del	disruptive_inframe_deletion	Exon 12 of 12	ENST00000341426.9	NP_075394.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NADK	ENST00000341426.9	c.1331_1336delAGGAGG	p.Glu444_Glu445del	disruptive_inframe_deletion	Exon 12 of 12	2	NM_023018.5	ENSP00000341679.5

Frequencies

GnomAD3 genomes AF: 0.000267 AC: 40 AN: 149844 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000489

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000666

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000198

Gnomad SAS AF: 0.000213

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000253

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000233 AC: 38 AN: 162868 AF XY: 0.000229

Gnomad AFR exome AF: 0.000584

Gnomad AMR exome AF: 0.0000424

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000355

Gnomad OTH exome AF: 0.000240

GnomAD4 exome AF: 0.000274 AC: 377 AN: 1375988 Hom.: 0 AF XY: 0.000277 AC XY: 189 AN XY: 682402

African (AFR) AF: 0.000306 AC: 10 AN: 32682

American (AMR) AF: 0.0000273 AC: 1 AN: 36638

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24792

East Asian (EAS) AF: 0.0000269 AC: 1 AN: 37174

South Asian (SAS) AF: 0.000160 AC: 13 AN: 81202

European-Finnish (FIN) AF: 0.0000206 AC: 1 AN: 48656

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5608

European-Non Finnish (NFE) AF: 0.000326 AC: 343 AN: 1052140

Other (OTH) AF: 0.000140 AC: 8 AN: 57096

GnomAD4 genome AF: 0.000267 AC: 40 AN: 149954 Hom.: 0 Cov.: 0 AF XY: 0.000219 AC XY: 16 AN XY: 73096

African (AFR) AF: 0.000487 AC: 20 AN: 41044

American (AMR) AF: 0.0000666 AC: 1 AN: 15024

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3454

East Asian (EAS) AF: 0.000199 AC: 1 AN: 5030

South Asian (SAS) AF: 0.000213 AC: 1 AN: 4692

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10218

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.000253 AC: 17 AN: 67234

Other (OTH) AF: 0.00 AC: 0 AN: 2064

Alfa AF: 0.000152 Hom.: 868

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.43
Mutation Taster		=124/76	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs71578334; hg19: chr1-1684347;