1-33012984-GCACACACA-GCA
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001625.4(AK2):c.*191_*196delTGTGTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000133 in 1,501,196 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 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 7.4e-7 ( 0 hom. )
Consequence
AK2
NM_001625.4 3_prime_UTR
NM_001625.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.53
Publications
0 publications found
Genes affected
AK2 (HGNC:362): (adenylate kinase 2) Adenylate kinases are involved in regulating the adenine nucleotide composition within a cell by catalyzing the reversible transfer of phosphate groups among adenine nucleotides. Three isozymes of adenylate kinase, namely 1, 2, and 3, have been identified in vertebrates; this gene encodes isozyme 2. Expression of these isozymes is tissue-specific and developmentally regulated. Isozyme 2 is localized in the mitochondrial intermembrane space and may play a role in apoptosis. Mutations in this gene are the cause of reticular dysgenesis. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 1 and 2.[provided by RefSeq, Nov 2010]
AK2 Gene-Disease associations (from GenCC):
- reticular dysgenesisInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Orphanet, Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001625.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| AK2 | NM_001625.4 | MANE Select | c.*191_*196delTGTGTG | 3_prime_UTR | Exon 6 of 6 | NP_001616.1 | P54819-1 | ||
| AK2 | NM_001319140.2 | c.*191_*196delTGTGTG | 3_prime_UTR | Exon 7 of 7 | NP_001306069.1 | P54819-6 | |||
| AK2 | NM_001319143.2 | c.*414_*419delTGTGTG | 3_prime_UTR | Exon 5 of 5 | NP_001306072.1 | G3V213 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| AK2 | ENST00000672715.1 | MANE Select | c.*191_*196delTGTGTG | 3_prime_UTR | Exon 6 of 6 | ENSP00000499935.1 | P54819-1 | ||
| AK2 | ENST00000354858.11 | TSL:1 | c.*191_*196delTGTGTG | 3_prime_UTR | Exon 5 of 5 | ENSP00000346921.7 | A0A5K1VW67 | ||
| AK2 | ENST00000373449.7 | TSL:1 | c.694+217_694+222delTGTGTG | intron | N/A | ENSP00000362548.2 | P54819-2 |
Frequencies
GnomAD3 genomes 0.00000665 AC: 1AN: 150438Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
150438
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 7.40e-7 AC: 1AN: 1350658Hom.: 0 AF XY: 0.00000149 AC XY: 1AN XY: 671338 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1
AN:
1350658
Hom.:
AF XY:
AC XY:
1
AN XY:
671338
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
30338
American (AMR)
AF:
AC:
0
AN:
40584
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24038
East Asian (EAS)
AF:
AC:
0
AN:
35934
South Asian (SAS)
AF:
AC:
0
AN:
79884
European-Finnish (FIN)
AF:
AC:
0
AN:
34568
Middle Eastern (MID)
AF:
AC:
0
AN:
5286
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1044308
Other (OTH)
AF:
AC:
0
AN:
55718
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.375
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00000664 AC: 1AN: 150538Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73528 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
150538
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
73528
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41114
American (AMR)
AF:
AC:
0
AN:
15120
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3442
East Asian (EAS)
AF:
AC:
1
AN:
5134
South Asian (SAS)
AF:
AC:
0
AN:
4764
European-Finnish (FIN)
AF:
AC:
0
AN:
10260
Middle Eastern (MID)
AF:
AC:
0
AN:
290
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67424
Other (OTH)
AF:
AC:
0
AN:
2080
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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