rs7924176

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006721.4(ADK):​c.726+10605A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,808 control chromosomes in the GnomAD database, including 9,181 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.31 ( 9181 hom., cov: 30)

Consequence

ADK
NM_006721.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.53

Publications

18 publications found
Variant links:
Genes affected
ADK (HGNC:257): (adenosine kinase) This gene an enzyme which catalyzes the transfer of the gamma-phosphate from ATP to adenosine, thereby serving as a regulator of concentrations of both extracellular adenosine and intracellular adenine nucleotides. Adenosine has widespread effects on the cardiovascular, nervous, respiratory, and immune systems and inhibitors of the enzyme could play an important pharmacological role in increasing intravascular adenosine concentrations and acting as anti-inflammatory agents. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2011]
ADK Gene-Disease associations (from GenCC):
  • adenosine kinase deficiency
    Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE, LIMITED Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P, ClinGen

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ADKNM_006721.4 linkc.726+10605A>G intron_variant Intron 7 of 10 ENST00000539909.6 NP_006712.2 P55263-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ADKENST00000539909.6 linkc.726+10605A>G intron_variant Intron 7 of 10 2 NM_006721.4 ENSP00000443965.2 P55263-1

Frequencies

GnomAD3 genomes
AF:
0.307
AC:
46619
AN:
151690
Hom.:
9183
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0962
Gnomad AMI
AF:
0.370
Gnomad AMR
AF:
0.306
Gnomad ASJ
AF:
0.551
Gnomad EAS
AF:
0.0206
Gnomad SAS
AF:
0.212
Gnomad FIN
AF:
0.339
Gnomad MID
AF:
0.396
Gnomad NFE
AF:
0.444
Gnomad OTH
AF:
0.366
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.307
AC:
46610
AN:
151808
Hom.:
9181
Cov.:
30
AF XY:
0.300
AC XY:
22270
AN XY:
74156
show subpopulations
African (AFR)
AF:
0.0960
AC:
3976
AN:
41422
American (AMR)
AF:
0.305
AC:
4653
AN:
15234
Ashkenazi Jewish (ASJ)
AF:
0.551
AC:
1911
AN:
3470
East Asian (EAS)
AF:
0.0205
AC:
106
AN:
5178
South Asian (SAS)
AF:
0.214
AC:
1024
AN:
4796
European-Finnish (FIN)
AF:
0.339
AC:
3551
AN:
10460
Middle Eastern (MID)
AF:
0.391
AC:
115
AN:
294
European-Non Finnish (NFE)
AF:
0.444
AC:
30174
AN:
67936
Other (OTH)
AF:
0.362
AC:
764
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1422
2844
4267
5689
7111
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
450
900
1350
1800
2250
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.404
Hom.:
54955
Bravo
AF:
0.295
Asia WGS
AF:
0.110
AC:
382
AN:
3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
9.4
DANN
Benign
0.76
PhyloP100
1.5
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs7924176; hg19: chr10-76295789; API