1-1752908-C-CCCT

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP3BP6_ModerateBA1

The NM_023018.5(NADK):​c.1334_1336dupAGG​(p.Glu445dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 1,525,002 control chromosomes in the GnomAD database, including 80,559 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.39 ( 13066 hom., cov: 0)
Exomes 𝑓: 0.40 ( 67493 hom. )

Consequence

NADK
NM_023018.5 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.315
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP3
Nonframeshift variant in repetitive region in NM_023018.5
BP6
Variant 1-1752908-C-CCCT is Benign according to our data. Variant chr1-1752908-C-CCCT is described in ClinVar as [Benign]. Clinvar id is 2672290.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NADKNM_023018.5 linkc.1334_1336dupAGG p.Glu445dup conservative_inframe_insertion Exon 12 of 12 ENST00000341426.9 NP_075394.3 O95544-1A0A024R058

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NADKENST00000341426.9 linkc.1334_1336dupAGG p.Glu445dup conservative_inframe_insertion Exon 12 of 12 2 NM_023018.5 ENSP00000341679.5 O95544-1

Frequencies

GnomAD3 genomes
AF:
0.392
AC:
58747
AN:
149740
Hom.:
13051
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.168
Gnomad AMI
AF:
0.551
Gnomad AMR
AF:
0.534
Gnomad ASJ
AF:
0.383
Gnomad EAS
AF:
0.373
Gnomad SAS
AF:
0.315
Gnomad FIN
AF:
0.475
Gnomad MID
AF:
0.363
Gnomad NFE
AF:
0.490
Gnomad OTH
AF:
0.407
GnomAD3 exomes
AF:
0.374
AC:
60843
AN:
162868
Hom.:
4553
AF XY:
0.370
AC XY:
32322
AN XY:
87258
show subpopulations
Gnomad AFR exome
AF:
0.145
Gnomad AMR exome
AF:
0.461
Gnomad ASJ exome
AF:
0.360
Gnomad EAS exome
AF:
0.329
Gnomad SAS exome
AF:
0.314
Gnomad FIN exome
AF:
0.418
Gnomad NFE exome
AF:
0.392
Gnomad OTH exome
AF:
0.397
GnomAD4 exome
AF:
0.395
AC:
543656
AN:
1375152
Hom.:
67493
Cov.:
39
AF XY:
0.390
AC XY:
265653
AN XY:
681934
show subpopulations
Gnomad4 AFR exome
AF:
0.146
Gnomad4 AMR exome
AF:
0.437
Gnomad4 ASJ exome
AF:
0.327
Gnomad4 EAS exome
AF:
0.319
Gnomad4 SAS exome
AF:
0.270
Gnomad4 FIN exome
AF:
0.410
Gnomad4 NFE exome
AF:
0.417
Gnomad4 OTH exome
AF:
0.377
GnomAD4 genome
AF:
0.392
AC:
58785
AN:
149850
Hom.:
13066
Cov.:
0
AF XY:
0.390
AC XY:
28486
AN XY:
73048
show subpopulations
Gnomad4 AFR
AF:
0.167
Gnomad4 AMR
AF:
0.535
Gnomad4 ASJ
AF:
0.383
Gnomad4 EAS
AF:
0.373
Gnomad4 SAS
AF:
0.316
Gnomad4 FIN
AF:
0.475
Gnomad4 NFE
AF:
0.490
Gnomad4 OTH
AF:
0.410

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
Dec 12, 2023
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: research

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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.

Other links and lift over

dbSNP: rs71578334; hg19: chr1-1684347; API