1-1752908-C-CCCT
Variant names:
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
NM_023018.5 conservative_inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.315
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]
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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 |
---|---|---|---|---|---|---|---|---|
NADK | NM_023018.5 | c.1334_1336dupAGG | p.Glu445dup | conservative_inframe_insertion | Exon 12 of 12 | ENST00000341426.9 | NP_075394.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.392 AC: 58747AN: 149740Hom.: 13051 Cov.: 0
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GnomAD3 exomes AF: 0.374 AC: 60843AN: 162868Hom.: 4553 AF XY: 0.370 AC XY: 32322AN XY: 87258
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GnomAD4 exome AF: 0.395 AC: 543656AN: 1375152Hom.: 67493 Cov.: 39 AF XY: 0.390 AC XY: 265653AN XY: 681934
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GnomAD4 genome AF: 0.392 AC: 58785AN: 149850Hom.: 13066 Cov.: 0 AF XY: 0.390 AC XY: 28486AN XY: 73048
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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
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at